@@ -332,7 +332,11 @@ is decoded and scanned

  * added CNSet class

  * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package)

-2009-11-19 R. Scharpf - committed version 1.5.6

+2009-11-19 R. Scharpf - committed version 1.5.6 

- * fixed bug in initialization of SnpCallSetPlus

+ * fixed bugs in initialization of SnpCallSetPlus

+

+2009-11-19 R. Scharpf - committed version 1.5.7

+

+ * fixed bugs in addFeatureAnnotation.SnpCallSetPlus

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

 Package: crlmm

 Type: Package

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

-Version: 1.5.6

+Version: 1.5.7

 Date: 2009-11-15

 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>

@@ -89,7 +89,7 @@ export(hmmOptions,

 export(ellipse) ##, ellipse.CopyNumberSet, getParam.SnpCallSetPlus)

 ##exportMethods(getParam)

-export(viterbi.CNSet, computeHmm.CNSet)

+export(viterbi.CNSet, computeHmm.CNSet, addFeatureAnnotation.SnpCallSetPlus)

@@ -1761,11 +1761,11 @@ addFeatureAnnotation.SnpCallSetPlus <- function(object, ...){

 				   isSnp[I]))

 	colnames(tmp.fd) <- c("chromosome", "position", "isSnp")

 	if("chromosome" %in% fvarLabels(object))

-		tmp.fd <- tmp.fd[ -1]

+		tmp.fd <- tmp.fd[, -1]

 	if("position" %in% fvarLabels(object))

-		tmp.fd <- tmp.fd[ -2]

+		tmp.fd <- tmp.fd[, -grep("position", colnames(tmp.fd)), drop=FALSE]

 	if("isSnp" %in% fvarLabels(object))

-		tmp.fd <- tmp.fd[ -3]

+		tmp.fd <- tmp.fd[, -grep("isSnp", colnames(tmp.fd)), drop=FALSE]

 	rownames(tmp.fd) <- featureNames(object)

 	tmp <- new("AnnotatedDataFrame",

 		   data=tmp.fd,