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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/crlmm@82282 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 31/10/2013 02:00:52 | ... | ... |
@@ -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: 1.20.0 |
|
| 5 |
-Date: Tue Oct 01 14:48:41 EDT 2013 |
|
| 4 |
+Version: 1.21.1 |
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| 5 |
+Date: Wed Oct 30 21:42:52 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: |
|
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+## time-stamp-pattern: "8/Date: %3a %3b %2d %02H:%02M:%02S %Z %:y\n" |
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+## End: |
| ... | ... |
@@ -371,12 +371,18 @@ RGtoXY = function(RG, chipType, verbose=TRUE) {
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| 371 | 371 |
bord = match(bids, featureNames(RG)) # and here |
| 372 | 372 |
# argrg = aids[rrgg] |
| 373 | 373 |
# brgrg = bids[rrgg] |
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+ xyPhenoData = AnnotatedDataFrame(data=RG@phenoData@data,varMetadata=RG@phenoData@varMetadata) |
|
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+ levels(xyPhenoData@varMetadata$channel) = c("X","Y","zero","_ALL_")
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|
| 374 | 376 |
XY <- new("NChannelSet",
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- X=matrix(0, nsnps, narrays), |
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- Y=matrix(0, nsnps, narrays), |
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- zero=matrix(0, nsnps, narrays), |
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- annotation=chipType, phenoData=RG@phenoData, |
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- protocolData=RG@protocolData, storage.mode="environment") |
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+ assayDataNew(X=matrix(0, nsnps, narrays),Y=matrix(0, nsnps, narrays),zero=matrix(0, nsnps, narrays)), |
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+ phenoData=xyPhenoData, protocolData=RG@protocolData, annotation=chipType) |
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+ storageMode(XY) = "environment" |
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+# XY <- new("NChannelSet",
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|
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+# X=matrix(0, nsnps, narrays), |
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+# Y=matrix(0, nsnps, narrays), |
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+# zero=matrix(0, nsnps, narrays), |
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+# annotation=chipType, phenoData=RG@phenoData, |
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+# protocolData=RG@protocolData, storage.mode="environment") |
|
| 380 | 386 |
featureNames(XY) = ids |
| 381 | 387 |
sampleNames(XY) = sampleNames(RG) |
| 382 | 388 |
## RS |
| ... | ... |
@@ -1352,7 +1358,7 @@ processIDAT <- function(stratum, sampleBatches, sampleSheet=NULL, |
| 1352 | 1358 |
A, B, |
| 1353 | 1359 |
GT, |
| 1354 | 1360 |
GTP, |
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- SKW, SNR, mixtureParams, is.snp) { #, outdir=".") {
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+ SKW, SNR, mixtureParams, is.snp) { #, outdir=".") {
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|
| 1356 | 1362 |
message("Processing sample stratum ", stratum, " of ", length(sampleBatches))
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| 1357 | 1363 |
sel <- sampleBatches[[stratum]] |
| 1358 | 1364 |
if(length(path)>= length(sel)) path = path[sel] |