git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@45172 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 11/03/2010 16:52:06 | ... | ... |
@@ -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: 1.5.34 |
|
| 4 |
+Version: 1.5.35 |
|
| 5 | 5 |
Date: 2010-02-05 |
| 6 | 6 |
Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.edu.au> |
| 7 | 7 |
Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU> |
| ... | ... |
@@ -54,7 +54,8 @@ getFeatureData.Affy <- function(cdfName, copynumber=FALSE){
|
| 54 | 54 |
##crlmmOpts$snpRange <- range(snpIndex) |
| 55 | 55 |
##crlmmOpts$npRange <- range(npIndex) |
| 56 | 56 |
} |
| 57 |
-construct <- function(filenames, cdfName, copynumber=FALSE, sns){
|
|
| 57 |
+construct <- function(filenames, cdfName, copynumber=FALSE, sns, verbose=TRUE){
|
|
| 58 |
+ if(verbose) message("Initializing container for assay data elements alleleA, alleleB, call, callProbability")
|
|
| 58 | 59 |
if(missing(sns)) sns <- basename(filenames) |
| 59 | 60 |
protocolData <- getProtocolData.Affy(filenames) |
| 60 | 61 |
featureData <- getFeatureData.Affy(cdfName, copynumber=copynumber) |
| ... | ... |
@@ -108,7 +109,8 @@ genotype <- function(filenames, cdfName, mixtureSampleSize=10^5, |
| 108 | 109 |
callSet <- construct(filenames=filenames, |
| 109 | 110 |
cdfName=cdfName, |
| 110 | 111 |
copynumber=copynumber, |
| 111 |
- sns=sns) |
|
| 112 |
+ sns=sns, |
|
| 113 |
+ verbose=verbose) |
|
| 112 | 114 |
mixtureParams <- matrix(NA, 4, length(filenames)) |
| 113 | 115 |
snp.index <- which(isSnp(callSet)==1) |
| 114 | 116 |
batches <- splitIndicesByLength(1:ncol(callSet), ocSamples()) |
| ... | ... |
@@ -122,7 +124,7 @@ genotype <- function(filenames, cdfName, mixtureSampleSize=10^5, |
| 122 | 124 |
cdfName=cdfName, |
| 123 | 125 |
sns=sns) |
| 124 | 126 |
stopifnot(identical(featureNames(callSet)[snp.index], snprmaRes$gns)) |
| 125 |
- message("Initializing container for assay data elements alleleA, alleleB, call, callProbability")
|
|
| 127 |
+ |
|
| 126 | 128 |
pData(callSet)$SKW[j] <- snprmaRes$SKW |
| 127 | 129 |
pData(callSet)$SNR[j] <- snprmaRes$SNR |
| 128 | 130 |
A(callSet)[snp.index, j] <- snprmaRes[["A"]] |