@@ -130,4 +130,10 @@ is decoded and scanned

 * fixed bug in cnrma

+2009-04-07 Rob Scharpf - committed versioni 1.0.78

+

+* added conf as argument to instantiateObjects

+

+

+

@@ -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: 1.0.77

+Version: 1.0.78

 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>

@@ -186,7 +186,7 @@ goodSnps <- function(phi.thr, envir, fewAA=20, fewBB=20){

 	return(flags)

 }

-instantiateObjects <- function(calls, NP, plate, envir, chrom, A, B,

+instantiateObjects <- function(calls, conf, NP, plate, envir, chrom, A, B,

 			       gender, SNRmin=5, SNR,

                                pkgname){

 	pkgname <- paste(pkgname, "Crlmm", sep="")

@@ -318,7 +318,7 @@ computeCopynumber <- function(chrom,

 	set.seed(seed)

 	if(missing(chrom)) stop("must specify chromosome")

 	if(length(ls(envir)) == 0) {

-		instantiateObjects(calls=calls, NP=NP, plate=plate,

+		instantiateObjects(calls=calls, conf=conf, NP=NP, plate=plate,

 				   envir=envir, chrom=chrom, A=A, B=B,

 				   gender=gender, SNR=SNR, SNRmin=SNRmin,

 				   pkgname=cdfName)