git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@58661 bc3139a8-67e5-0310-9ffc-ced21a209358
Rob Scharp authored on 01/10/2011 04:50:07
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@@ -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. |
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-Version: 1.11.37 |
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+Version: 1.11.38 |
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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> |
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@@ -29,7 +29,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs, |
| 29 | 29 |
"A<-", "B<-", open, close, flags, |
| 30 | 30 |
openff, closeff, |
| 31 | 31 |
batchStatistics, "batchStatistics<-", updateObject, |
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- order, checkOrder) |
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+ order, checkOrder, snpNames) |
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importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles, |
| 34 | 34 |
copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded) |
| 35 | 35 |
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@@ -9,6 +9,18 @@ getProtocolData.Affy <- function(filenames){
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| 9 | 9 |
row.names=colnames(scanDates))) |
| 10 | 10 |
return(protocoldata) |
| 11 | 11 |
} |
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+ |
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+setMethod("snpNames", signature(object="character"),
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+ function(object){
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+ nm <- grep("Crlmm", object)
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+ if(length(nm)==0){
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+ pkgname <- paste(object, "Crlmm", sep="") |
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+ } else pkgname <- object |
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+ loader("preprocStuff.rda", .crlmmPkgEnv, object)
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+ gns <- getVarInEnv("gns")
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+ return(gns) |
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+ }) |
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+ |
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| 12 | 24 |
getFeatureData <- function(cdfName, copynumber=FALSE){
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| 13 | 25 |
pkgname <- getCrlmmAnnotationName(cdfName) |
| 14 | 26 |
if(!require(pkgname, character.only=TRUE)){
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@@ -2,7 +2,7 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
| 2 | 2 |
col.names=NULL, probs=c(1/3, 1/3, 1/3), DF=6, |
| 3 | 3 |
SNRMin=5, recallMin=10, recallRegMin=1000, |
| 4 | 4 |
gender=NULL, desctrucitve=FALSE, verbose=TRUE, |
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- returnParams=FALSE, badSNP=.7, snp.names){
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+ returnParams=FALSE, badSNP=.7){
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pkgname <- getCrlmmAnnotationName(cdfName) |
| 7 | 7 |
stopifnot(require(pkgname, character.only=TRUE, quietly=!verbose)) |
| 8 | 8 |
open(SNR) |
| ... | ... |
@@ -18,11 +18,14 @@ crlmmGT2 <- function(A, B, SNR, mixtureParams, cdfName, row.names=NULL, |
| 18 | 18 |
stopifnot(nrow(A) == length(gns)) |
| 19 | 19 |
index <- seq(length=nrow(A)) |
| 20 | 20 |
} |
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- if(!missing(snp.names)){
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- stopifnot(!is.null(rownames(A))) |
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- ##verify that A has only snps. otherwise, calling function must pass rownames |
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- index <- match(snp.names, rownames(A)) |
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- } |
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+ snp.names <- snpNames(pkgname) |
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+ stopifnot(!is.null(rownames(A))) |
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+ index <- match(snp.names, rownames(A)) |
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+## if(!missing(snp.names)){
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+## |
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+## ##verify that A has only snps. otherwise, calling function must pass rownames |
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+## index <- match(snp.names, rownames(A)) |
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+## } |
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snpBatches <- splitIndicesByLength(index, ocProbesets()) |
| 27 | 30 |
NR <- length(unlist(snpBatches)) |
| 28 | 31 |
if(verbose) message("Calling ", NR, " SNPs for recalibration... ")
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