Browse code

Cleaning up... importing isPackageLoaded() from oligoClasses

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/crlmm@51994 bc3139a8-67e5-0310-9ffc-ced21a209358

Benilton Carvalho authored on 20/01/2011 18:33:39
Showing3 changed files

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@@ -1,7 +1,7 @@
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 Package: crlmm
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 Type: Package
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 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: 1.9.10
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+Version: 1.9.2
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 Date: 2010-12-10
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 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
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 Maintainer: Benilton S Carvalho <Benilton.Carvalho@cancer.org.uk>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>
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@@ -32,7 +32,7 @@ importMethodsFrom(oligoClasses, allele, calls, "calls<-", confs,
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 		  "A<-", "B<-", open, close, flags,
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 		  batchStatistics, "batchStatistics<-", updateObject)
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 importFrom(oligoClasses, chromosome2integer, celfileDate, list.celfiles,
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-           copyNumber, initializeBigMatrix, initializeBigVector)
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+           copyNumber, initializeBigMatrix, initializeBigVector, isPackageLoaded)
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 importFrom(graphics, abline, axis, layout, legend, mtext, par, plot,
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@@ -94,9 +94,6 @@ list2SnpSet <- function(x, returnParams=FALSE){
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                           "Center AA", "Center AB", "Center BB",
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                           "Scale AA", "Scale AB", "Scale BB",
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                           "N AA", "N AB", "N BB"),
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-#                          "Shift in parameters AA",
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-#                          "Shift in parameters AB",
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-#                          "Shift in parameters BB"),
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                         row.names=c(
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                           "SNPQC",
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                           "cAA", "cAB", "cBB",
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@@ -142,8 +139,7 @@ loader <- function(theFile, envir, pkgname){
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 celDates <- function(celfiles){
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 	if(!all(file.exists(celfiles))) stop("1 or more cel file does not exist")
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-	celdates <- vector("character", length(celfiles))
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-	celtimes <- vector("character", length(celfiles))
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+	celdates <- celtimes <- vector("character", length(celfiles))
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 	for(i in seq(along=celfiles)){
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 		if(i %% 100 == 0) cat(".")
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 		tmp <- read.celfile.header(celfiles[i], info="full")$DatHeader
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@@ -172,19 +168,12 @@ validCdfNames <- function(){
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           "humanimmuno12v1b")
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 }
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 isValidCdfName <- function(cdfName){
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-	chipList <- validCdfNames()
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-	result <- cdfName %in% chipList	
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-	if(!(result)){
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-		warning("cdfName must be one of the following: ",
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-			chipList)
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-	}
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-	return(result)
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-}
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-
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-isPackageLoaded <- function(pkg){
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-	stopifnot(is.character(pkg))
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-	pkg <- paste("package:", pkg, sep="")
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-	pkg %in% search()
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+    stopifnot(is.character(cdfName))
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+    result <- cdfName %in% validCdfNames()
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+    if (!result)
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+        warning("cdfName must be one of the following: ",
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+                chipList)
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+    return(result)
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 }
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 paramNames <- function(){