* 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
| ... | ... |
@@ -38,12 +38,12 @@ citEntry(entry="article", |
| 38 | 38 |
"Aravinda Chakravarti and", |
| 39 | 39 |
"Rafael A Irizarry"), |
| 40 | 40 |
journal = "Biostatistics", |
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- year = "2010", |
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- volume="", |
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- pages="", |
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+ year = "2011", |
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+ volume="12", |
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+ pages="33--50", |
|
| 44 | 44 |
textVersion = paste("Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA",
|
| 45 | 45 |
"A multilevel model to address batch effects in copy number estimation using SNP arrays", |
| 46 |
- "Biostatistics. 2010.")) |
|
| 46 |
+ "Biostatistics. 2011.")) |
|
| 47 | 47 |
|
| 48 | 48 |
citEntry(entry = "Article", |
| 49 | 49 |
title = "Using the {R} Package {crlmm} for Genotyping and Copy Number Estimation",
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@55182 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 30/04/2011 11:38:33
| ... | ... |
@@ -45,8 +45,6 @@ citEntry(entry="article", |
| 45 | 45 |
"A multilevel model to address batch effects in copy number estimation using SNP arrays", |
| 46 | 46 |
"Biostatistics. 2010.")) |
| 47 | 47 |
|
| 48 |
-citHeader("To cite crlmm in publications use:")
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|
| 49 |
- |
|
| 50 | 48 |
citEntry(entry = "Article", |
| 51 | 49 |
title = "Using the {R} Package {crlmm} for Genotyping and Copy Number Estimation",
|
| 52 | 50 |
author = personList(as.person("Robert B. Scharpf"),
|
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@55179 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 30/04/2011 01:50:04
| ... | ... |
@@ -1,6 +1,6 @@ |
| 1 | 1 |
citHeader("To cite crlmm in publications use:")
|
| 2 | 2 |
|
| 3 |
-citEntry(entry="article", |
|
| 3 |
+citEntry(entry="article", |
|
| 4 | 4 |
title = "Quantifying uncertainty in genotype calls", |
| 5 | 5 |
author = paste("Benilton S Carvalho and",
|
| 6 | 6 |
"Thomas A Louis and", |
| ... | ... |
@@ -13,7 +13,7 @@ citEntry(entry="article", |
| 13 | 13 |
"Quantifying uncertainty in genotype calls.", |
| 14 | 14 |
"Bioinformatics. 2010 Jan 15;26(2):242-9.")) |
| 15 | 15 |
|
| 16 |
-citEntry(entry="article", |
|
| 16 |
+citEntry(entry="article", |
|
| 17 | 17 |
title = "R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips", |
| 18 | 18 |
author = paste("Matthew E Ritchie and",
|
| 19 | 19 |
"Benilton S Carvalho and", |
| ... | ... |
@@ -28,7 +28,7 @@ citEntry(entry="article", |
| 28 | 28 |
"R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.", |
| 29 | 29 |
"Bioinformatics. 2009 Oct 1;25(19):2621-3.")) |
| 30 | 30 |
|
| 31 |
-citEntry(entry="article", |
|
| 31 |
+citEntry(entry="article", |
|
| 32 | 32 |
title = "A multilevel model to address batch effects in copy number estimation |
| 33 | 33 |
using SNP arrays", |
| 34 | 34 |
author = paste("Robert B Scharpf and",
|
| ... | ... |
@@ -45,6 +45,29 @@ citEntry(entry="article", |
| 45 | 45 |
"A multilevel model to address batch effects in copy number estimation using SNP arrays", |
| 46 | 46 |
"Biostatistics. 2010.")) |
| 47 | 47 |
|
| 48 |
+citHeader("To cite crlmm in publications use:")
|
|
| 49 |
+ |
|
| 50 |
+citEntry(entry = "Article", |
|
| 51 |
+ title = "Using the {R} Package {crlmm} for Genotyping and Copy Number Estimation",
|
|
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+ author = personList(as.person("Robert B. Scharpf"),
|
|
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+ as.person("Rafael A. Irizarry"),
|
|
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+ as.person("Matthew E. Ritchie"),
|
|
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+ as.person("Benilton Carvalho"),
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|
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+ as.person("Ingo Ruczinski")),
|
|
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+ journal = "Journal of Statistical Software", |
|
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+ year = "2011", |
|
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+ volume = "40", |
|
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+ number = "12", |
|
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+ pages = "1--32", |
|
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+ url = "http://www.jstatsoft.org/v40/i12/", |
|
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+ |
|
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+ textVersion = |
|
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+ paste("Robert B. Scharpf, Rafael A. Irizarry, Matthew E. Ritchie, Benilton Carvalho, Ingo Ruczinski (2011).",
|
|
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+ "Using the R Package crlmm for Genotyping and Copy Number Estimation.", |
|
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+ "Journal of Statistical Software, 40(12), 1-32.", |
|
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+ "URL http://www.jstatsoft.org/v40/i12/.") |
|
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+) |
|
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+ |
|
| 48 | 71 |
|
| 49 | 72 |
citFooter("We have invested a lot of time and effort in creating crlmm,",
|
| 50 | 73 |
"please cite it when using it for data analysis.") |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@48627 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 02/08/2010 08:52:27
| ... | ... |
@@ -28,6 +28,23 @@ citEntry(entry="article", |
| 28 | 28 |
"R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.", |
| 29 | 29 |
"Bioinformatics. 2009 Oct 1;25(19):2621-3.")) |
| 30 | 30 |
|
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+citEntry(entry="article", |
|
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+ title = "A multilevel model to address batch effects in copy number estimation |
|
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+ using SNP arrays", |
|
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+ author = paste("Robert B Scharpf and",
|
|
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+ "Ingo Ruczinski and", |
|
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+ "Benilton Carvalho and", |
|
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+ "Betty Doan and", |
|
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+ "Aravinda Chakravarti and", |
|
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+ "Rafael A Irizarry"), |
|
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+ journal = "Biostatistics", |
|
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+ year = "2010", |
|
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+ volume="", |
|
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+ pages="", |
|
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+ textVersion = paste("Scharpf RB, Ruczinski I, Carvalho B, Doan B, Chakravarti A, Irizarry RA",
|
|
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+ "A multilevel model to address batch effects in copy number estimation using SNP arrays", |
|
| 46 |
+ "Biostatistics. 2010.")) |
|
| 47 |
+ |
|
| 31 | 48 |
|
| 32 | 49 |
citFooter("We have invested a lot of time and effort in creating crlmm,",
|
| 33 | 50 |
"please cite it when using it for data analysis.") |
git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45608 bc3139a8-67e5-0310-9ffc-ced21a209358
Benilton Carvalho authored on 31/03/2010 11:16:26
| 1 | 1 |
new file mode 100644 |
| ... | ... |
@@ -0,0 +1,34 @@ |
| 1 |
+citHeader("To cite crlmm in publications use:")
|
|
| 2 |
+ |
|
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+citEntry(entry="article", |
|
| 4 |
+ title = "Quantifying uncertainty in genotype calls", |
|
| 5 |
+ author = paste("Benilton S Carvalho and",
|
|
| 6 |
+ "Thomas A Louis and", |
|
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+ "Rafael A Irizarry"), |
|
| 8 |
+ journal = "Bioinformatics", |
|
| 9 |
+ year = "2010", |
|
| 10 |
+ volume = "15;26(2)", |
|
| 11 |
+ pages = "242-9", |
|
| 12 |
+ textVersion = paste("Carvalho BS, Louis TA, Irizarry RA.",
|
|
| 13 |
+ "Quantifying uncertainty in genotype calls.", |
|
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+ "Bioinformatics. 2010 Jan 15;26(2):242-9.")) |
|
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+ |
|
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+citEntry(entry="article", |
|
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+ title = "R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips", |
|
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+ author = paste("Matthew E Ritchie and",
|
|
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+ "Benilton S Carvalho and", |
|
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+ "Kurt N Hetrick and", |
|
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+ "Simon Tavar\'e and", |
|
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+ "Rafael A Irizarry"), |
|
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+ journal = "Bioinformatics", |
|
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+ year = "2009", |
|
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+ volume = "25(19)", |
|
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+ pages = "2621-3", |
|
| 27 |
+ textVersion = paste("Ritchie ME, Carvalho BS, Hetrick KN, Tavar\'e S.",
|
|
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+ "R/Bioconductor software for Illumina's Infinium whole-genome genotyping BeadChips.", |
|
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+ "Bioinformatics. 2009 Oct 1;25(19):2621-3.")) |
|
| 30 |
+ |
|
| 31 |
+ |
|
| 32 |
+citFooter("We have invested a lot of time and effort in creating crlmm,",
|
|
| 33 |
+ "please cite it when using it for data analysis.") |
|
| 34 |
+ |