@@ -124,4 +124,10 @@ is decoded and scanned

 * fixed bug in cnrma

+2009-04-07 Rob Scharpf - committed versioni 1.0.77

+

+* cnrma accepts other cdfNames

+

+* fixed bug in cnrma

+

@@ -1,7 +1,7 @@

 Package: crlmm

 Type: Package

 Title: Genotype Calling (CRLMM) and Copy Number Analysis tool for SNP 5.0 and 6.0 arrays.

-Version: 1.0.76

+Version: 1.0.77

 Date: 2008-12-30

 Author: Rafael A Irizarry, Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

 Maintainer: Benilton S Carvalho <bcarvalh@jhsph.edu>, Robert Scharpf <rscharpf@jhsph.edu>, Matt Ritchie <mritchie@wehi.EDU.AU>

@@ -128,17 +128,11 @@ celDates <- function(celfiles){

 }

 cnrma <- function(filenames, cdfName="genomewidesnp6", sns, seed=1, verbose=FALSE){

-	if(cdfName != "genomewidesnp6") stop("Only genomewidesnp6 supported at this time")

-	## BC: 03/14/09

-	## getting pkgname from cdfName, in the future this might be useful

-	## as the method might be implemented for other platforms

 	pkgname <- getCrlmmAnnotationName(cdfName)

 	require(pkgname, character.only=TRUE) || stop("Package ", pkgname, " not available")

 	if (missing(sns)) sns <- basename(filenames)

-	## Loading data in .crlmmPkgEnv and extracting from there

         loader("npProbesFid.rda", .crlmmPkgEnv, pkgname)

-##	data("npProbesFid", package=pkgname, envir=.crlmmPkgEnv)

-	fid <- getVarInEnv("fid")

+	fid <- getVarInEnv("npProbesFid")

 	set.seed(seed)

 	idx2 <- sample(length(fid), 10^5) ##for skewness. no need to do everything

 	SKW <- vector("numeric", length(filenames))

@@ -148,9 +142,7 @@ cnrma <- function(filenames, cdfName="genomewidesnp6", sns, seed=1, verbose=FALS

 		message("Processing ", length(filenames), " files.")

 		if (getRversion() > '2.7.0') pb <- txtProgressBar(min=0, max=length(filenames), style=3)

 	}

-	##load reference distribution obtained from hapmap

         loader("1m_reference_cn.rda", .crlmmPkgEnv, pkgname)

-##	data(list="1m_reference_cn", package="genomewidesnp6Crlmm", envir=.crlmmPkgEnv)

 	reference <- getVarInEnv("reference")

 	for(i in seq(along=filenames)){

 		y <- as.matrix(read.celfile(filenames[i], intensity.means.only=TRUE)[["INTENSITY"]][["MEAN"]][fid])