1. crlmm
  2. DESCRIPTION
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:04:22
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DESCRIPTION
History View file @5bac5c8
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.56.0
5 
+Version: 1.57.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_16 branch

J Wokaty authored on 01/11/2022 15:04:22
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DESCRIPTION
History View file @90f1862
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.55.0
5 
+Version: 1.56.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:02:46
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DESCRIPTION
History View file @94edd96
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.54.0
5 
+Version: 1.55.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_15 branch

Nitesh Turaga authored on 26/04/2022 15:02:46
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DESCRIPTION
History View file @1eefa13
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.53.0
5 
+Version: 1.54.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:53:43
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DESCRIPTION
History View file @8ed9c38
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.52.0
5 
+Version: 1.53.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_14 branch

Nitesh Turaga authored on 26/10/2021 15:53:43
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DESCRIPTION
History View file @9ecc85f
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.51.0
5 
+Version: 1.52.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:42:53
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DESCRIPTION
History View file @26229e6
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.50.0
5 
+Version: 1.51.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_13 branch

Nitesh Turaga authored on 19/05/2021 15:42:53
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DESCRIPTION
History View file @c3560d3
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.49.1
5 
+Version: 1.50.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

remove GGdata from suggests

rscharpf authored on 01/12/2020 15:51:33
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DESCRIPTION
History View file @b690225
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.49.0
5 
+Version: 1.49.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
... ... 
@@ -19,7 +19,7 @@ Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 19 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
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         matrixStats, VGAM, parallel, graphics, limma, beanplot
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-Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
22 
+Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), snpStats,
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         RUnit
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 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
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         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
... ... 
@@ -27,7 +27,8 @@ Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
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         crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R
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         snprma-functions.R utils.R zzz.R test_crlmm_package.R
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 LazyLoad: yes
30 
-## Local Variables:
30 
+## Local Variables:
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 ## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
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-## End:
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+## End:
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 biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
34 
+RoxygenNote: 7.1.1
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:35:27
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DESCRIPTION
History View file @88433a9
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.48.0
5 
+Version: 1.49.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_12 branch

Nitesh Turaga authored on 27/10/2020 14:35:27
Showing1 changed files
DESCRIPTION
History View file @bb8c119
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.47.0
5 
+Version: 1.48.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to odd y following creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:19:05
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DESCRIPTION
History View file @4d09e85
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.46.0
5 
+Version: 1.47.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_11 branch

Nitesh Turaga authored on 27/04/2020 18:19:05
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DESCRIPTION
History View file @162ee9a
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.45.0
5 
+Version: 1.46.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Remove dependency on SNPchip

rscharpf authored on 23/11/2019 12:40:06
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DESCRIPTION
History View file @a836381
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@@ -16,7 +16,7 @@ Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
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         1.17.7)
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 LinkingTo: preprocessCore (>= 1.17.7)
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 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 
-        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
19 
+        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
21 21 
         matrixStats, VGAM, parallel, graphics, limma, beanplot
22 22 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
Browse code

bump x.y.z version to odd y after creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:34:55
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DESCRIPTION
History View file @f00f0ce
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.44.0
5 
+Version: 1.45.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z version to even y prior to creation of RELEASE_3_10 branch

Nitesh Turaga authored on 29/10/2019 17:08:04
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DESCRIPTION
History View file @6f0bbea
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.43.0
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+Version: 1.44.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 16:10:49
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DESCRIPTION
History View file @813feae
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
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-Version: 1.42.0
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+Version: 1.43.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_9 branch

Nitesh Turaga authored on 02/05/2019 15:53:11
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DESCRIPTION
History View file @7054c21
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.41.0
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+Version: 1.42.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:54:28
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DESCRIPTION
History View file @090f347
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.40.0
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+Version: 1.41.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_8 branch

vobencha authored on 30/10/2018 15:41:45
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DESCRIPTION
History View file @95b6fe6
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.39.1
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+Version: 1.40.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

replace BiocInstaller biocLite mentions with BiocManager

LiNk-NY authored on 30/08/2018 17:47:04
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DESCRIPTION
History View file @7b66dd2
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.39.0
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+Version: 1.39.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:41:37
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DESCRIPTION
History View file @125b018
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.38.0
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+Version: 1.39.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_7 branch

vobencha authored on 30/04/2018 14:35:10
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DESCRIPTION
History View file @cc1a98e
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.37.1
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+Version: 1.38.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Bug fixes to illumina genotype calling when using cdfName="nopackage" option

mritchie authored on 19/04/2018 07:17:14
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DESCRIPTION
History View file @d49c960
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.37.0
5 
+Version: 1.37.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:52:08
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DESCRIPTION
History View file @5bf92ab
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.36.0
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+Version: 1.37.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of RELEASE_3_6 branch

Hervé Pagès authored on 30/10/2017 16:39:25
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DESCRIPTION
History View file @150e13b
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.35.0
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+Version: 1.36.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd y after creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@129129 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:50:57
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DESCRIPTION
History View file @e1264a4
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.34.0
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+Version: 1.35.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even y prior to creation of 3_5 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@129126 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 24/04/2017 19:25:24
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DESCRIPTION
History View file @17c862f
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
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-Version: 1.33.1
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+Version: 1.34.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Updated DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126742 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/02/2017 07:24:29
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DESCRIPTION
History View file @73c9e5b
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.33.2
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+Version: 1.33.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Updated DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126740 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 14/02/2017 05:45:37
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DESCRIPTION
History View file @9411738
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@@ -2,7 +2,7 @@ Package: crlmm
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.33.0
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+Version: 1.33.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to odd 'y' after creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@122712 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 19:10:43
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.32.0
5 
+Version: 1.33.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

bump x.y.z versions to even 'y' prior to creation of 3_4 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@122710 bc3139a8-67e5-0310-9ffc-ced21a209358

Herve Pages authored on 17/10/2016 18:45:06
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
-Version: 1.31.2
5 
+Version: 1.32.0
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Added SNP plotting functions

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117175 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 06/05/2016 06:53:13
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 
-        Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.31.1
4 
+        Affymetrix SNP 5.0 and 6.0 and Illumina arrays
5 
+Version: 1.31.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
... ... 
@@ -10,7 +10,7 @@ Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
10 10 
         <mritchie@wehi.EDU.AU>
11 11 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
12 12 
         arrays, as well as a copy number tool specific to 5.0, 6.0, and
13 
-        Illumina platforms
13 
+        Illumina platforms.
14 14 
 License: Artistic-2.0
15 15 
 Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
16 16 
         1.17.7)
Browse code

Also added some new plotting options and updated version number

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117088 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:41:15
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.31.0
5 
+Version: 1.31.1
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Added nopackage option for krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117087 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/05/2016 23:39:54
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@@ -18,13 +18,13 @@ LinkingTo: preprocessCore (>= 1.17.7)
18 18 
 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
19 19 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
20 20 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
21 
-        matrixStats, VGAM, parallel
21 
+        matrixStats, VGAM, parallel, graphics, limma, beanplot
22 22 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
23 23 
         RUnit
24 24 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
25 25 
         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
26 26 
         methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
27 
-        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
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+        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R
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         snprma-functions.R utils.R zzz.R test_crlmm_package.R
29 29 
 LazyLoad: yes
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 ## Local Variables:
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bump version after creating 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117081 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:30:44
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2 2 
 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.30.0
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+Version: 1.31.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Bump versions prior to creation of 3.3 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117079 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/05/2016 21:20:18
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.29.2
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+Version: 1.30.0
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

replace reference to texi2dvi with pdflatex as the former has been removed from MikTex

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112478 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 12/01/2016 20:52:19
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.29.1
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+Version: 1.29.2
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
7 7 
         Ruczinski, Rafael A Irizarry
8 8 
 Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
Browse code

Fixing contact information

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112282 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 07/01/2016 20:29:51
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@@ -2,11 +2,10 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.29.0
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-Date: Sat Oct 18 14:34:17 EST 2014
5 
+Version: 1.29.1
7 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 7 
         Ruczinski, Rafael A Irizarry
9 
-Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
8 
+Maintainer: Benilton S Carvalho <benilton@unicamp.br>,
10 9 
         Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
11 10 
         <mritchie@wehi.EDU.AU>
12 11 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
Browse code

Bumped version number of all packages after creation of 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109592 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:59:53
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.28.0
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+Version: 1.29.0
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 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bumped versions of all packages prior to creating 3.2 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109589 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2015 19:36:05
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.27.0
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+Version: 1.28.0
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 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump versions in trunk after creation of 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102594 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 20:02:44
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.26.0
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+Version: 1.27.0
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 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump versions prior to creating 3.1 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102591 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/04/2015 19:42:01
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2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.25.1
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+Version: 1.26.0
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 Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

bug fix to krlmm

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@101808 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 03/04/2015 00:01:45
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.25.0
6 
-Date: Thu Sep 25 21:06:19 EST 2014
5 
+Version: 1.25.1
6 
+Date: Sat Oct 18 14:34:17 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Bumping versions after creating 3.0 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95443 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:47:41
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.24.0
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+Version: 1.25.0
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 Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Bump package versions prior to creating the 3.0 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95439 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 13/10/2014 21:38:33
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@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.23.4
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+Version: 1.24.0
6 6 
 Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Added support for humanexome12v1.2a chip

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94521 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 25/09/2014 11:06:52
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.3
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-Date: Fri Sep 19 10:10:31 EDT 2014
5 
+Version: 1.23.4
6 
+Date: Thu Sep 25 21:06:19 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 736588e3d47fd58358f61ce2241bb2c85b4d9a0c

update to vignette to process previously unevaluated codechunks

Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-09-19 10:14:04 -0400
Author date: 2014-09-19 10:14:04 -0400


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94285 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/09/2014 14:22:04
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.2
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-Date: Mon Aug 25 21:43:53 EDT 2014
5 
+Version: 1.23.3
6 
+Date: Fri Sep 19 10:10:31 EDT 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Commit made by the Bioconductor Git-SVN bridge. Consists of 1 commit.

Commit information:

Commit id: 7a7b52509b1e09bf8d3f517244f90f9045d102ca
Commit message: Set enough.men and enough.women to FALSE by default in fit.lm3 function.
Committed by: Rob Scharpf
Author Name: Rob Scharpf
Commit date: 2014-08-25 21:44:19 -0400
Author date: 2014-08-25 21:44:19 -0400



git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@93599 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 26/08/2014 01:45:03
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.1
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-Date: Mon 10 Jun 2014 15:10:27 EST
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+Version: 1.23.2
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+Date: Mon Aug 25 21:43:53 EDT 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Changed tolerance allowed for reading in arrays with different numbers of probes (was 10000, now 4% of total number of probes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@91227 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/06/2014 23:43:33
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@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.23.0
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-Date: Mon 31 Mar 2014 18:08:54 EST
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+Version: 1.23.1
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+Date: Mon 10 Jun 2014 15:10:27 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
... ... 
@@ -19,7 +19,7 @@ LinkingTo: preprocessCore (>= 1.17.7)
19 19 
 Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
20 20 
         1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
21 21 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 
-        matrixStats, VGAM
22 
+        matrixStats, VGAM, parallel
23 23 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 24 
         RUnit
25 25 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
Browse code

Second version bump after creating 2.14 release branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88840 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:21:21
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 Type: Package
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.22.0
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+Version: 1.23.0
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 Date: Mon 31 Mar 2014 18:08:54 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

First version bump prior to creating 2.14 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88838 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 11/04/2014 21:07:21
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
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-Version: 1.21.9
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 Date: Mon 31 Mar 2014 18:08:54 EST
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
Browse code

Changes to krlmm to avoid error that occurs in k-means clustering when all intensities are identical

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88225 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 01/04/2014 02:51:49
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 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
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-Version: 1.21.8
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-Date: Fri Mar 28 16:26:10 EST 2014
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+Version: 1.21.9
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+Date: Mon 31 Mar 2014 18:08:54 EST
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 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

Removed crlmm::: from .R files and set saveDate=FALSE in genotype.Illumina() man page to clean up Notes and Warnings

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88085 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 28/03/2014 12:43:01
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History View file @1e41609
... ... 
@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.7
6 
-Date: Mon Mar 10 10:06:36 EST 2014
5 
+Version: 1.21.8
6 
+Date: Fri Mar 28 16:26:10 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
... ... 
@@ -21,7 +21,7 @@ Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
21 21 
         utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 22 
         matrixStats, VGAM
23 23 
 Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 
-        ellipse, RUnit, VGAM
24 
+        RUnit
25 25 
 Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
26 26 
         methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
27 27 
         methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
Browse code

Added back support for human1mv1c chip (accidentally deleted)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@87249 bc3139a8-67e5-0310-9ffc-ced21a209358

unknown authored on 10/03/2014 04:38:28
Showing1 changed files
DESCRIPTION
History View file @b2dc56d
... ... 
@@ -2,8 +2,8 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 4 
         Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
-Version: 1.21.6
6 
-Date: Mon Feb 3 09:02:42 EST 2014
5 
+Version: 1.21.7
6 
+Date: Mon Mar 10 10:06:36 EST 2014
7 7 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 8 
         Ruczinski, Rafael A Irizarry
9 9 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
Browse code

modify to new biocViews to DESCRIPTION file

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@87035 bc3139a8-67e5-0310-9ffc-ced21a209358

Sonali Arora authored on 04/03/2014 22:12:21
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DESCRIPTION
History View file @d94b2bc
... ... 
@@ -1,58 +1,34 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 
-Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.5
5 
-Date: Mon Feb  3 09:02:42 EST 2014
6 
-Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 
-Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 
-Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
3 
+Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for
4 
+        Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
5 
+Version: 1.21.6
6 
+Date: Mon Feb 3 09:02:42 EST 2014
7 
+Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo
8 
+        Ruczinski, Rafael A Irizarry
9 
+Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>,
10 
+        Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie
11 
+        <mritchie@wehi.EDU.AU>
12 
+Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0
13 
+        arrays, as well as a copy number tool specific to 5.0, 6.0, and
14 
+        Illumina platforms
9 15 
 License: Artistic-2.0
10 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7)
16 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>=
17 
+        1.17.7)
11 18 
 LinkingTo: preprocessCore (>= 1.17.7)
12 
-Imports: methods,
13 
-         Biobase (>= 2.15.4),
14 
-         BiocGenerics,
15 
-         affyio (>= 1.23.2),
16 
-         illuminaio,
17 
-         ellipse,
18 
-         mvtnorm,
19 
-         splines,
20 
-         stats,
21 
-         SNPchip,
22 
-         utils,
23 
-	 lattice,
24 
-	 ff,
25 
-	 foreach,
26 
-         RcppEigen (>= 0.3.1.2.1),
27 
-	 matrixStats,
28 
-	 VGAM
29 
-Suggests: hapmapsnp6,
30 
-          genomewidesnp6Crlmm (>= 1.0.7),
31 
-          GGdata,
32 
-          snpStats,
33 
-	  ellipse,
34 
-	  RUnit,
35 
-	  VGAM
36 
-Collate: AllGenerics.R
37 
-	 AllClasses.R
38 
-	 methods-AssayData.R
39 
-	 methods-CNSet.R
40 
-	 methods-CNSetLM.R
41 
-	 methods-eSet.R
42 
-         methods-SnpSuperSet.R
43 
-	 methods-PredictionRegion.R
44 
-         cnrma-functions.R
45 
-	 cnset-accessors.R
46 
-         crlmm-functions.R
47 
-	 crlmmGT2.R
48 
-         crlmm-illumina.R
49 
-         krlmm.R
50 
-	 snprma-functions.R
51 
-         utils.R
52 
-         zzz.R
53 
-	 test_crlmm_package.R
19 
+Imports: methods, Biobase (>= 2.15.4), BiocGenerics, affyio (>=
20 
+        1.23.2), illuminaio, ellipse, mvtnorm, splines, stats, SNPchip,
21 
+        utils, lattice, ff, foreach, RcppEigen (>= 0.3.1.2.1),
22 
+        matrixStats, VGAM
23 
+Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats,
24 
+        ellipse, RUnit, VGAM
25 
+Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R
26 
+        methods-CNSetLM.R methods-eSet.R methods-SnpSuperSet.R
27 
+        methods-PredictionRegion.R cnrma-functions.R cnset-accessors.R
28 
+        crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R
29 
+        snprma-functions.R utils.R zzz.R test_crlmm_package.R
54 30 
 LazyLoad: yes
55 
-biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 31 
 ## Local Variables:
57 32 
 ## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 33 
 ## End:
34 
+biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation
Browse code

bumped version as all packages that depend on Rcpp must be rebuilt

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86058 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 04/02/2014 18:07:39
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DESCRIPTION
History View file @8bfebd1
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.4
4 
+Version: 1.21.5
5 5 
 Date: Mon Feb  3 09:02:42 EST 2014
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

merged matt's changes on the collab branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86002 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 03/02/2014 14:03:16
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DESCRIPTION
History View file @c27ba9c
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.21.1
5 
-Date: Wed Oct 30 21:42:52 EDT 2013
4 
+Version: 1.21.4
5 
+Date: Mon Feb  3 09:02:42 EST 2014
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

version bump

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82281 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:39
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DESCRIPTION
History View file @eaa7924
... ... 
@@ -1,13 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-<<<<<<< HEAD
5 
-Version: 1.21.0
6 
-Date: Wed Oct 30 21:27:01 EDT 2013
7 
-=======
8 
-Version: 1.19.9
9 
-Date: Fri Oct 25 14:00:41 EDT 2013
10 
->>>>>>> 9a92fa5d0719c007647a5b14c24201d277db3f1b
4 
+Version: 1.21.1
5 
+Date: Wed Oct 30 21:42:52 EDT 2013
11 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
12 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
13 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

fix bug in construction of NChannelSet

- thanks to Alex Baras for finding and supplying patch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82280 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:34
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DESCRIPTION
History View file @4d398a2
... ... 
@@ -1,8 +1,13 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
+<<<<<<< HEAD
4 5 
 Version: 1.21.0
5 6 
 Date: Wed Oct 30 21:27:01 EDT 2013
7 
+=======
8 
+Version: 1.19.9
9 
+Date: Fri Oct 25 14:00:41 EDT 2013
10 
+>>>>>>> 9a92fa5d0719c007647a5b14c24201d277db3f1b
6 11 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 12 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 13 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merge with upstream change made at bioc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82279 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/10/2013 01:45:27
Showing1 changed files
DESCRIPTION
History View file @34a5a07
... ... 
@@ -2,7 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 4 
 Version: 1.21.0
5 
-Date: Tue Oct 01 14:48:41 EDT 2013
5 
+Date: Wed Oct 30 21:27:01 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -53,3 +53,6 @@ Collate: AllGenerics.R
53 53 
 	 test_crlmm_package.R
54 54 
 LazyLoad: yes
55 55 
 biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
+## Local Variables:
57 
+## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
+## End:
Browse code

bump version after release branch has been created

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81644 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:47:19
Showing1 changed files
DESCRIPTION
History View file @dfcb149
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.20.0
4 
+Version: 1.21.0
5 5 
 Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

bump versions prior to creating BioC 2.13 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81642 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 14/10/2013 21:29:21
Showing1 changed files
DESCRIPTION
History View file @291177d
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.8
4 
+Version: 1.20.0
5 5 
 Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

merge with collab

* collab:
Update DESCRIPTION
bug fixed for krlmm option, documentation changes

es

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81002 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 01/10/2013 12:03:56
Showing1 changed files
DESCRIPTION
History View file @1d875d3
... ... 
@@ -1,8 +1,8 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.7
5 
-Date: Mon Sep 30 10:06:41 EDT 2013
4 
+Version: 1.19.8
5 
+Date: Tue Oct 01 14:48:41 EDT 2013
6 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -53,6 +53,3 @@ Collate: AllGenerics.R
53 53 
 	 test_crlmm_package.R
54 54 
 LazyLoad: yes
55 55 
 biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
-## Local Variables:
57 
-## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
-## End:
Browse code

fix conflict in description

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@80947 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/09/2013 14:07:17
Showing1 changed files
DESCRIPTION
History View file @ba1a7d7
... ... 
@@ -2,6 +2,7 @@ Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 4 
 Version: 1.19.7
5 
+Date: Mon Sep 30 10:06:41 EDT 2013
5 6 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 8 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -23,13 +24,15 @@ Imports: methods,
23 24 
 	 ff,
24 25 
 	 foreach,
25 26 
          RcppEigen (>= 0.3.1.2.1),
26 
-	 matrixStats
27 
+	 matrixStats,
28 
+	 VGAM
27 29 
 Suggests: hapmapsnp6,
28 30 
           genomewidesnp6Crlmm (>= 1.0.7),
29 31 
           GGdata,
30 32 
           snpStats,
31 33 
 	  ellipse,
32 
-	  RUnit
34 
+	  RUnit,
35 
+	  VGAM
33 36 
 Collate: AllGenerics.R
34 37 
 	 AllClasses.R
35 38 
 	 methods-AssayData.R
... ... 
@@ -49,4 +52,7 @@ Collate: AllGenerics.R
49 52 
          zzz.R
50 53 
 	 test_crlmm_package.R
51 54 
 LazyLoad: yes
52 
-biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
55 
+biocViews: Microarray, Preprocessing, SNP, Bioinformatics,CopyNumberVariants
56 
+## Local Variables:
57 
+## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n"
58 
+## End:
Browse code

fix syntax error

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79516 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 16/08/2013 22:34:26
Showing1 changed files
DESCRIPTION
History View file @71f28ae
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.6
4 
+Version: 1.19.7
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merging from collab

* collab:
add warning in vignette about NAs with BafLrrSetList function
Added Human Omni Express Exome 8 v1.1b as a supported chip
updated version number of pacakge and man pages to reflect these changes
skeleton for krlmm capability added. genotype.Illumina() can now take and XY object as input
update copynumber.Rnw to use BafLrrSetList
updates to vignettes
update namespace

# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@79138 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 31/07/2013 01:37:34
Showing1 changed files
DESCRIPTION
History View file @808cfec
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.2
4 
+Version: 1.19.6
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
... ... 
@@ -22,7 +22,7 @@ Imports: methods,
22 22 
 	 lattice,
23 23 
 	 ff,
24 24 
 	 foreach,
25 
-         RcppEigen,
25 
+         RcppEigen (>= 0.3.1.2.1),
26 26 
 	 matrixStats
27 27 
 Suggests: hapmapsnp6,
28 28 
           genomewidesnp6Crlmm (>= 1.0.7),
... ... 
@@ -43,6 +43,7 @@ Collate: AllGenerics.R
43 43 
          crlmm-functions.R
44 44 
 	 crlmmGT2.R
45 45 
          crlmm-illumina.R
46 
+         krlmm.R
46 47 
 	 snprma-functions.R
47 48 
          utils.R
48 49 
          zzz.R
Browse code

bumped version

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@77033 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/05/2013 17:42:28
Showing1 changed files
DESCRIPTION
History View file @a963512
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.1
4 
+Version: 1.19.2
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

bump version number from svn repo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@77032 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 30/05/2013 17:37:29
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.19.0
4 
+Version: 1.19.1
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Bump y in version x.y.z to odd number in devel

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@75270 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 22:06:11
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.18.0
4 
+Version: 1.19.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

bump y of x.y.z version number for BioC 2.12 release

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@75263 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 03/04/2013 21:32:27
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.15
4 
+Version: 1.18.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

update namespace

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72808 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/01/2013 05:14:35
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.14
4 
+Version: 1.17.15
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merge local changes with dan's changes on bioc

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72708 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/01/2013 18:31:47
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.12
4 
+Version: 1.17.14
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.21.4), preprocessCore (>= 1.17.7)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= 1.17.7)
10 10 
 LinkingTo: preprocessCore (>= 1.17.7)
11 11 
 Imports: methods,
12 12 
          Biobase (>= 2.15.4),
13 13 
          BiocGenerics,
14 14 
          affyio (>= 1.23.2),
15 
+         illuminaio,
15 16 
          ellipse,
16 
-         genefilter (>= 1.37.1),
17 17 
          mvtnorm,
18 18 
          splines,
19 19 
          stats,
... ... 
@@ -22,9 +22,10 @@ Imports: methods,
22 22 
 	 lattice,
23 23 
 	 ff,
24 24 
 	 foreach,
25 
-         RcppEigen
25 
+         RcppEigen,
26 
+	 matrixStats
26 27 
 Suggests: hapmapsnp6,
27 
-          genomewidesnp6Crlmm (>= 1.0.4),
28 
+          genomewidesnp6Crlmm (>= 1.0.7),
28 29 
           GGdata,
29 30 
           snpStats,
30 31 
 	  ellipse,
Browse code

@<- has been moved from methods to base, so it no longer needs to be imported in package NAMESPACEs.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@72298 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 04/01/2013 21:18:09
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.11
4 
+Version: 1.17.12
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

merge collab branch

* collab:
update vignettes/Makefile
update .gitignore
update table in CopyNumberViewiew
bump dependency on oligoClasses version
Update alias for "[" method for PredictionRegion objects
Replaced CopyNumberOverview and Infrastructure vignettes with those in the release branch. The versions in release have removed AffymetrixPreprocessCN, which is no longer available

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71322 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/11/2012 04:49:34
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@@ -1,12 +1,12 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.9
4 
+Version: 1.17.11
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39), preprocessCore (>= 1.17.7)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.21.4), preprocessCore (>= 1.17.7)
10 10 
 LinkingTo: preprocessCore (>= 1.17.7)
11 11 
 Imports: methods,
12 12 
          Biobase (>= 2.15.4),
Browse code

merge with collab branch containing fix for dqrls and bug-fix for computeRBaf that can misalign sample index with batch index (when batch is not in alphabetical order)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@71295 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/11/2012 15:24:46
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@@ -1,12 +1,13 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.1
4 
+Version: 1.17.9
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39), preprocessCore (>= 1.17.7)
10 
+LinkingTo: preprocessCore (>= 1.17.7)
10 11 
 Imports: methods,
11 12 
          Biobase (>= 2.15.4),
12 13 
          BiocGenerics,
... ... 
@@ -14,14 +15,14 @@ Imports: methods,
14 15 
          ellipse,
15 16 
          genefilter (>= 1.37.1),
16 17 
          mvtnorm,
17 
-         preprocessCore (>= 1.17.7),
18 18 
          splines,
19 19 
          stats,
20 20 
          SNPchip,
21 21 
          utils,
22 22 
 	 lattice,
23 23 
 	 ff,
24 
-	 foreach
24 
+	 foreach,
25 
+         RcppEigen
25 26 
 Suggests: hapmapsnp6,
26 27 
           genomewidesnp6Crlmm (>= 1.0.4),
27 28 
           GGdata,
Browse code

don't need to call texi2dvi explicitly in Makefile, plus it doesn't work in Windows

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@70209 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 04/10/2012 22:30:56
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.17.0
4 
+Version: 1.17.1
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

bump package versions after creating 2.11 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@70052 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:43:56
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.16.0
4 
+Version: 1.17.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Bump all packages before creating 2.11 branch.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@70050 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 01/10/2012 22:16:24
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1 1 
 Package: crlmm
2 2 
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3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.31
4 
+Version: 1.16.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Merge branch 'collab'

* collab:
remove *.pdf from vignettes/ (these are built by the package checker)
update .gitignore
add inst/scripts/crlmmDownstream.pdf
bump version
Add crlmmIllumina.pdf

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69643 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/09/2012 00:05:45
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1 1 
 Package: crlmm
2 2 
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3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.30
4 
+Version: 1.15.31
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Merge branch 'collab'

* collab:
Update AffyGW.pdf and IlluminaPreprocessCN.pdf
crlmmIlluminaV2 calls crlmmGT. comment call to crlmmGT2
Update AffyGW vignette to step through construction of CNSet, normalization, and genotyping
v 1.15.27: Fix bug in crlmmGT2. clean up comments in crlmmIllumina.
update getFeatureData

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69561 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/09/2012 12:31:51
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.25
4 
+Version: 1.15.30
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Merge branch 'collab'

* collab:
update Rds
revert imputeGender to original api
bug fix for calculateRBafCNSet
update calculateRBafCNSet
Fix documentation for crlmmCopynumber -- added argument fitLinearModel
update crlmmGT2
Put rm(DD, ...) further down in crlmmGT2 function
remove message about cloning A and B
Open and close callsPr and callsGt in crlmmGT2 (when args not missing)
revert removed indices loaded in crlmmGT2
snprmaAffy no longer writes normalized intensities to calls and callProbability slots. crlmmGT2 takes arguments callsGt and callsPr. When present, crlmmGT2 will not overwrite A and B.
explicit coercion to matrix in imputeGender
Assign imputed gender to cnSet$gender within crlmmGT2 function.
Change sum(SNR > SNRmin) to sum(SNR[] > SNRmin) in imputeGender

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@69450 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 14/09/2012 20:07:37
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@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.18
4 
+Version: 1.15.25
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Merge branch 'collab'

* collab:
Update CNSet objects in data/ with datadir slot and protocolData(object)$filename
update cnrmaAffy. processCEL2 located inside cnrmaAffy function. Uses lexical scope.
Change API for genotypeAffy -- remove mixtureParams argument. Update call to genotypeAffy in genotype function
snprmaAffy no longer initializes mixtureParams object, but accesses this information from the cnSet
constructAffyCNSet initializes mixtureParams slot of the appropriate dimensions
updated cnrmaAffy. Removed cnrma2, cnrma. cnrmaAffy uses lexical scope
Fix bug in crlmmGT2 caused by unequal batch sizes
Moved rsprocessCel inside of snprmaAffy for lexical scope. Moved imputeGender inside crlmmGT2 for lexical scope
Revert imputeGender to original approach for crlmm. Splitting samples across nodes does not work well if there are not a lot of samples in the individual nodes. Probably better to use fewer markers on chr X when large number of samples are processed
contains old process1 call
change gender <- unlist(gender) to gender <- unlist(genderList)
v1.15.15 Fix memory leak in imputeGender step by running this function in sample batches of size ocSamples(). Use lexical scope in calling process1 function in crlmmGT2.
set default values in summarizeNps
depends on v 1.19.39 of oligoClasses
v1.15.14: Export constructAffyCNSet. Used datadir slot in CNSet object added to v 1.19.39 of oligoClasses
update getFeatureData for use with annotation package that contains a number of SNPs not necessarily included in the genotyping. These additional snps are removed when constructing the featureData in constructAffy

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67826 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 19/07/2012 03:57:08
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1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.12
4 
+Version: 1.15.18
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.19.17)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.19.39)
10 10 
 Imports: methods,
11 11 
          Biobase (>= 2.15.4),
12 12 
          BiocGenerics,
Browse code

Merge branch 'collab'

* collab: (34 commits)
revert change to IlluminaPreprocessCN
fix bug in isValidCdfName
print warning when all features in a batch of probes are flagged, but allow processing to continue
add utility cleancdfnames
Add validCdfNames.Rd
export validCdfNames
imputeGender fix when chromosome Y not available
Use splitIndicesByLength(index, ocSamples/getDoParWorkers())
Can not allocate vector of size XG with genotype.Illumina. Use splitIndicesByNode() only if the length of the list is greater than the split from splitIndicesByLength(). Otherwise, split by length using ocSamples()
update .gitignore
Add make.unique for sampleSheet$Sample_ID in readIdatFiles
bug in description
ensure sample ids stored in samplesheet are unique when constructing cnSet object
update oligoClasses dependency
update unit test for genotype.Illumina
revert change in constructInf call from genotype.Illumina
Update genotype.Rd
edit ACN function
1.15.6 use make.unique(basename(arrayNames)) to allow processing of Illumina samples with duplicated barcodes
check that sample identifies are unique in crlmm function
...

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@67435 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/07/2012 19:00:03
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DESCRIPTION
History View file @063b3d1
... ... 
@@ -1,12 +1,12 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.15.0
4 
+Version: 1.15.12
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0), oligoClasses (>= 1.17.36)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.19.17)
10 10 
 Imports: methods,
11 11 
          Biobase (>= 2.15.4),
12 12 
          BiocGenerics,
... ... 
@@ -20,7 +20,8 @@ Imports: methods,
20 20 
          SNPchip,
21 21 
          utils,
22 22 
 	 lattice,
23 
-	 ff
23 
+	 ff,
24 
+	 foreach
24 25 
 Suggests: hapmapsnp6,
25 26 
           genomewidesnp6Crlmm (>= 1.0.4),
26 27 
           GGdata,
Browse code

bumped version numbers after creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64680 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:15:56
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DESCRIPTION
History View file @f1691f7
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.14.0
4 
+Version: 1.15.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

first version bump prior to creating 2.10 branch

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64678 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 30/03/2012 22:05:02
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DESCRIPTION
History View file @276f140
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.19
4 
+Version: 1.14.0
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
Browse code

Merge branch 'collab'

* collab:
fixing vignettes dir
fixing vignettes dir
removing old vignettes
removing old vignettes
Adding GGdata to suggests
Fixed vignette for genotyping + association; Moved oligoClasses back to Depends b/c final users do need access to calls()/confs() when using crlmm()

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64350 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 17:35:35
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DESCRIPTION
History View file @2124212
... ... 
@@ -1,15 +1,14 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.14
4 
+Version: 1.13.19
5 5 
 Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
6 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
7 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
8 8 
 License: Artistic-2.0
9 
-Depends: R (>= 2.14.0)
9 
+Depends: R (>= 2.14.0), oligoClasses (>= 1.17.36)
10 10 
 Imports: methods,
11 11 
          Biobase (>= 2.15.4),
12 
-         oligoClasses (>= 1.17.36),
13 12 
          BiocGenerics,
14 13 
          affyio (>= 1.23.2),
15 14 
          ellipse,
... ... 
@@ -24,6 +23,7 @@ Imports: methods,
24 23 
 	 ff
25 24 
 Suggests: hapmapsnp6,
26 25 
           genomewidesnp6Crlmm (>= 1.0.4),
26 
+          GGdata,
27 27 
           snpStats,
28 28 
 	  ellipse,
29 29 
 	  RUnit
Browse code

Merge branch 'collab'

* collab:
bump version
made cnSetExample smaller. Fix notes
Trying to revert bad commit
remove cn-functions. update description
comment most of cn-functions.r
Resaved rdas
update data/cnSetExample.rda and data/cnSetExample2.rda
bump version
coercion method from CNSet to oligoSnpSet makes integer matrices of BAFs and lrr's
import ff_or_matrix from oligoClasses. bump dependency on oligoClasses version. Use library(oligoClasses) in some of the crlmm examples.
Cleaning pkg loading process: work still required
move Biobase and methods to imports

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64324 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 23/03/2012 03:34:50
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DESCRIPTION
History View file @ad3cc70
... ... 
@@ -1,21 +1,21 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.12
5 
-Date: 2010-12-10
6 
-Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
4 
+Version: 1.13.14
5 
+Author: Benilton S Carvalho, Robert Scharpf, Matt Ritchie, Ingo Ruczinski, Rafael A Irizarry
7 6 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
8 7 
 Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms
9 8 
 License: Artistic-2.0
10 
-Depends: R (>= 2.13.0),
11 
-         methods,
12 
-         Biobase (>= 2.15.0),
13 
-         oligoClasses (>= 1.17.34)
14 
-Imports: affyio (>= 1.19.2),
9 
+Depends: R (>= 2.14.0)
10 
+Imports: methods,
11 
+         Biobase (>= 2.15.4),
12 
+         oligoClasses (>= 1.17.36),
13 
+         BiocGenerics,
14 
+         affyio (>= 1.23.2),
15 15 
          ellipse,
16 
-         genefilter (>= 1.33.0),
16 
+         genefilter (>= 1.37.1),
17 17 
          mvtnorm,
18 
-         preprocessCore (>= 1.13.4),
18 
+         preprocessCore (>= 1.17.7),
19 19 
          splines,
20 20 
          stats,
21 21 
          SNPchip,
... ... 
@@ -41,10 +41,8 @@ Collate: AllGenerics.R
41 41 
 	 crlmmGT2.R
42 42 
          crlmm-illumina.R
43 43 
 	 snprma-functions.R
44 
-	 cn-functions.R
45 44 
          utils.R
46 45 
          zzz.R
47 46 
 	 test_crlmm_package.R
48 47 
 LazyLoad: yes
49 48 
 biocViews: Microarray, Preprocessing, SNP, Bioinformatics, CopyNumberVariants
50 
-Packaged: 2011-04-30 17:10:59 UTC; biocbuild
51 49 
\ No newline at end of file
Browse code

Merge branch 'collab'

* collab:
remove getCluster() calls and replace with parStatus()
update man pages for crlmm and genotype.Illumina with respect to the setup for parallelization
add neededPkgs argument to ocLapply calls in crlmmGT2
bump dependency on oligoClasses
Update R/crlmm-illumina.R
contructInf, preprocessInf and genotypeInf no longer exported

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64211 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 21/03/2012 02:52:50
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DESCRIPTION
History View file @3d15962
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.11
4 
+Version: 1.13.12
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
... ... 
@@ -10,7 +10,7 @@ License: Artistic-2.0
10 10 
 Depends: R (>= 2.13.0),
11 11 
          methods,
12 12 
          Biobase (>= 2.15.0),
13 
-         oligoClasses (>= 1.17.29)
13 
+         oligoClasses (>= 1.17.34)
14 14 
 Imports: affyio (>= 1.19.2),
15 15 
          ellipse,
16 16 
          genefilter (>= 1.33.0),
Browse code

Merge branch 'collab'

* collab:
replace splitIndicesByLength with splitIndicesByNode throughout cnrma-functions.R (check that snow is loaded and getCluster is not null)
add an example to genotype.Illumina that indicates how parallelization would be enabled. The example requires local data and is not run.
change outdir in IlluminaPreprocessCN and AffyGW
Update R/crlmm-illumina.R
bump version for parallelization of genotype.Illumina
Update R/crlmm-illumina.R

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@64151 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 20/03/2012 13:55:50
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History View file @a139404
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.10
4 
+Version: 1.13.11
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

Merge branch 'collab'

* collab:
update cnSet objects in data/
bump version
update version dependencies
coerce copy number and bafs to integer matrix in setAs(CNSet, oligoSnpSet)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@63707 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 10/03/2012 00:05:37
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DESCRIPTION
History View file @621f08e
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.9
4 
+Version: 1.13.10
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
... ... 
@@ -9,8 +9,8 @@ Description: Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays,
9 9 
 License: Artistic-2.0
10 10 
 Depends: R (>= 2.13.0),
11 11 
          methods,
12 
-         Biobase (>= 2.11.9),
13 
-         oligoClasses (>= 1.15.41)
12 
+         Biobase (>= 2.15.0),
13 
+         oligoClasses (>= 1.17.29)
14 14 
 Imports: affyio (>= 1.19.2),
15 15 
          ellipse,
16 16 
          genefilter (>= 1.33.0),
Browse code

Merge branch 'collab'

* collab:
bump crlmm version
add alias for coercing CNSet to oligoSnpSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62631 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 08/02/2012 13:58:34
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History View file @ae93295
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.8
4 
+Version: 1.13.9
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

Merge branch 'collab'

* collab:
coercion of CNSet to oligoSnpSet uses lrr/baf instead of ca+cb/genotypes

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62557 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 05/02/2012 15:20:45
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DESCRIPTION
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... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.7
4 
+Version: 1.13.8
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
Browse code

Merge branch 'mymac'

* mymac:
add AffyGW.pdf
update vignettes in inst/scripts
Change argument of validCEL to celfiles
Update constructInf to accommodate GenomeDataFrame class for featureData
bump version to 1.13.7
Add doRUnit.R
Add celfile-utils.Rd
Streamlne some of the Rd files
add validCEL function that checks whether all celfiles can be read
getFeatureData returns GenomeAnnotatedDataFrame
Remove imports from methods. Remove pdf of illumina_copynumber.pdf (large file) and copynumber.pdf
getFeatureDAta returns GenomeAnnotatedDataFrame
Remove separate vignette for copy number in inst/scripts. Include copynumber section in both affy and illumina pipelines.
update documentation files for genotype.Illumina, preprocessInf, and genotypeInf (cdfName added as argument. Indicate that 'batch' should be a character string)
pass cdfName to genotypeInf and preprocessInf
add unitTests and cn-functions for 'simple usage'
Combine AffyPreprocess and copynumber. Combine IlluminaPreprocess and copynumber
remove depency on ff to allow installation on my mac

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@62108 bc3139a8-67e5-0310-9ffc-ced21a209358

Rob Scharp authored on 17/01/2012 19:13:44
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DESCRIPTION
History View file @7c0c9ac
... ... 
@@ -1,7 +1,7 @@
1 1 
 Package: crlmm
2 2 
 Type: Package
3 3 
 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for Affymetrix SNP 5.0 and 6.0 and Illumina arrays.
4 
-Version: 1.13.5
4 
+Version: 1.13.7
5 5 
 Date: 2010-12-10
6 6 
 Author: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au>, Ingo Ruczinski <iruczins@jhsph.edu>, Rafael A Irizarry
7 7 
 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
... ... 
@@ -14,20 +14,19 @@ Depends: R (>= 2.13.0),
14 14 
 Imports: affyio (>= 1.19.2),
15 15 
          ellipse,
16 16 
          genefilter (>= 1.33.0),
17