git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@53657 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 12/03/2011 19:56:02
| ... | ... |
@@ -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: 1.9.18 |
|
| 4 |
+bVersion: 1.9.19 |
|
| 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> |
| ... | ... |
@@ -1160,9 +1160,10 @@ genotype.Illumina <- function(sampleSheet=NULL, |
| 1160 | 1160 |
highDensity=highDensity, sep=sep, fileExt=fileExt, |
| 1161 | 1161 |
cdfName=cdfName, copynumber=copynumber, verbose=verbose, batch=batch, # fns=fns, |
| 1162 | 1162 |
saveDate=saveDate) #, outdir=outdir) |
| 1163 |
+ sampleNames(callSet) <- basename(sampleNames(callSet)) |
|
| 1163 | 1164 |
save(callSet, file=file.path(ldPath(), "callSet.rda")) |
| 1164 | 1165 |
} else message("Using callSet loaded from GlobalEnv")
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| 1165 |
- if(missing(sns)) sns = sampleNames(callSet) |
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| 1166 |
+ if(missing(sns)) sns = basename(sampleNames(callSet)) |
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| 1166 | 1167 |
if(is.lds) {
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| 1167 | 1168 |
open(A(callSet)) |
| 1168 | 1169 |
open(B(callSet)) |
| ... | ... |
@@ -1227,10 +1228,8 @@ genotype.Illumina <- function(sampleSheet=NULL, |
| 1227 | 1228 |
open(B(callSet)) |
| 1228 | 1229 |
tmpA = initializeBigMatrix(name="tmpA", length(snp.index), narrays) |
| 1229 | 1230 |
tmpB = initializeBigMatrix(name="tmpB", length(snp.index), narrays) |
| 1230 |
- ## bb = getOption("ffbatchbytes")
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|
| 1231 |
- ## bb = ocProbesets()*length(sns)*8 |
|
| 1232 |
- ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet)) #, BATCHBYTES=bb) # X=A(callSet)[snp.index,] |
|
| 1233 |
- ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet)) #, BATCHBYTES=bb) # X=B(callSet)[snp.index,] |
|
| 1231 |
+ ffcolapply(tmpA[,i1:i2] <- A(callSet)[snp.index,i1:i2], X=A(callSet)) |
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| 1232 |
+ ffcolapply(tmpB[,i1:i2] <- B(callSet)[snp.index,i1:i2], X=B(callSet)) |
|
| 1234 | 1233 |
close(A(callSet)) |
| 1235 | 1234 |
close(B(callSet)) |
| 1236 | 1235 |
close(tmpA) |
| ... | ... |
@@ -1254,6 +1253,9 @@ genotype.Illumina <- function(sampleSheet=NULL, |
| 1254 | 1253 |
## verbose, |
| 1255 | 1254 |
## returnParams, |
| 1256 | 1255 |
## badSNP)) |
| 1256 |
+ save(tmpA, file=file.path(ldPath(), "tmpA.rda")) |
|
| 1257 |
+ save(tmpB, file=file.path(ldPath(), "tmpB.rda")) |
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| 1258 |
+ save(mixtureParams, file=file.path(ldPath(), "mixtureParams.rda")) |
|
| 1257 | 1259 |
tmp <- crlmmGTfxn(FUN, |
| 1258 | 1260 |
A=tmpA, |
| 1259 | 1261 |
B=tmpB, |