... | ... |
@@ -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: 1.60.0 |
|
5 |
+Version: 1.61.0 |
|
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>, |
... | ... |
@@ -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: 1.59.0 |
|
5 |
+Version: 1.60.0 |
|
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>, |
... | ... |
@@ -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: 1.58.0 |
|
5 |
+Version: 1.59.0 |
|
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>, |
... | ... |
@@ -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: 1.57.0 |
|
5 |
+Version: 1.58.0 |
|
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>, |
... | ... |
@@ -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: 1.56.0 |
|
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>, |
... | ... |
@@ -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: 1.55.0 |
|
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>, |
... | ... |
@@ -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: 1.54.0 |
|
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>, |
... | ... |
@@ -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: 1.53.0 |
|
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>, |
... | ... |
@@ -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: 1.52.0 |
|
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>, |
... | ... |
@@ -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: 1.51.0 |
|
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>, |
... | ... |
@@ -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: 1.50.0 |
|
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>, |
... | ... |
@@ -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: 1.49.1 |
|
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>, |
... | ... |
@@ -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: 1.49.0 |
|
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), |
21 | 21 |
matrixStats, VGAM, parallel, graphics, limma, beanplot |
22 |
-Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, |
|
22 |
+Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), 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 |
... | ... |
@@ -27,7 +27,8 @@ Collate: AllGenerics.R AllClasses.R methods-AssayData.R methods-CNSet.R |
27 | 27 |
crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R |
28 | 28 |
snprma-functions.R utils.R zzz.R test_crlmm_package.R |
29 | 29 |
LazyLoad: yes |
30 |
-## Local Variables: |
|
30 |
+## Local Variables: |
|
31 | 31 |
## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n" |
32 |
-## End: |
|
32 |
+## End: |
|
33 | 33 |
biocViews: Microarray, Preprocessing, SNP, CopyNumberVariation |
34 |
+RoxygenNote: 7.1.1 |
... | ... |
@@ -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: 1.48.0 |
|
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>, |
... | ... |
@@ -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>, |
... | ... |
@@ -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: 1.46.0 |
|
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>, |
... | ... |
@@ -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: 1.45.0 |
|
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>, |
... | ... |
@@ -16,7 +16,7 @@ Depends: R (>= 2.14.0), oligoClasses (>= 1.21.12), preprocessCore (>= |
16 | 16 |
1.17.7) |
17 | 17 |
LinkingTo: preprocessCore (>= 1.17.7) |
18 | 18 |
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, |
... | ... |
@@ -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: 1.44.0 |
|
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>, |
... | ... |
@@ -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: 1.43.0 |
|
5 |
+Version: 1.44.0 |
|
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>, |
... | ... |
@@ -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: 1.42.0 |
|
5 |
+Version: 1.43.0 |
|
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>, |
... | ... |
@@ -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: 1.41.0 |
|
5 |
+Version: 1.42.0 |
|
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>, |
... | ... |
@@ -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: 1.40.0 |
|
5 |
+Version: 1.41.0 |
|
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>, |
... | ... |
@@ -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: 1.39.1 |
|
5 |
+Version: 1.40.0 |
|
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>, |
... | ... |
@@ -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: 1.39.0 |
|
5 |
+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>, |
... | ... |
@@ -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: 1.38.0 |
|
5 |
+Version: 1.39.0 |
|
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>, |
... | ... |
@@ -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: 1.37.1 |
|
5 |
+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>, |
... | ... |
@@ -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: 1.37.0 |
|
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>, |
... | ... |
@@ -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: 1.36.0 |
|
5 |
+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>, |
... | ... |
@@ -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: 1.35.0 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@129129 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.34.0 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@129126 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.33.1 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126742 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.33.2 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@126740 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.33.0 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@122712 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.32.0 |
|
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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@122710 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.31.2 |
|
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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117175 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -1,8 +1,8 @@ |
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) |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117088 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.31.0 |
|
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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117087 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
|
27 |
+ crlmm-functions.R crlmmGT2.R crlmm-illumina.R krlmm.R plot.R |
|
28 | 28 |
snprma-functions.R utils.R zzz.R test_crlmm_package.R |
29 | 29 |
LazyLoad: yes |
30 | 30 |
## Local Variables: |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117081 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.30.0 |
|
5 |
+Version: 1.31.0 |
|
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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@117079 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.29.2 |
|
5 |
+Version: 1.30.0 |
|
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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112478 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.29.1 |
|
5 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@112282 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
|
6 |
-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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109592 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.28.0 |
|
5 |
+Version: 1.29.0 |
|
6 | 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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@109589 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.27.0 |
|
5 |
+Version: 1.28.0 |
|
6 | 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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102594 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.26.0 |
|
5 |
+Version: 1.27.0 |
|
6 | 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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@102591 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.25.1 |
|
5 |
+Version: 1.26.0 |
|
6 | 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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@101808 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95443 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.24.0 |
|
5 |
+Version: 1.25.0 |
|
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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@95439 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.23.4 |
|
5 |
+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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@94521 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
|
6 |
-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>, |
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
... | ... |
@@ -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 |
|
6 |
-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>, |
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
... | ... |
@@ -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 |
|
6 |
-Date: Mon 10 Jun 2014 15:10:27 EST |
|
5 |
+Version: 1.23.2 |
|
6 |
+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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@91227 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.23.0 |
|
6 |
-Date: Mon 31 Mar 2014 18:08:54 EST |
|
5 |
+Version: 1.23.1 |
|
6 |
+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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88840 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.22.0 |
|
5 |
+Version: 1.23.0 |
|
6 | 6 |
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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88838 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.21.9 |
|
5 |
+Version: 1.22.0 |
|
6 | 6 |
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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88225 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: 1.21.8 |
|
6 |
-Date: Fri Mar 28 16:26:10 EST 2014 |
|
5 |
+Version: 1.21.9 |
|
6 |
+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 |
9 | 9 |
Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@88085 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@87249 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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>, |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@87035 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86058 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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> |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@86002 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82281 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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 |
- 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
... | ... |
@@ -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 |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@82279 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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: |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81644 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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> |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@81642 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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> |
* 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
... | ... |
@@ -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: |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@80947 bc3139a8-67e5-0310-9ffc-ced21a209358
... | ... |
@@ -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, |
|
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+ VGAM |
|
27 | 29 |
Suggests: hapmapsnp6, |
28 | 30 |
genomewidesnp6Crlmm (>= 1.0.7), |
29 | 31 |
GGdata, |
30 | 32 |
snpStats, |
31 | 33 |
ellipse, |
32 |
- RUnit |
|
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+ RUnit, |
|
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+ 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: |
|