Browse code

updated construct function with verbose arg

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
Showing2 changed files

... ...
@@ -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"]]