scoreMatrixList.R:

	- changed & -> && when testing for the file

R/scoreMatrixList.R

@@ -101,7 +101,7 @@ ScoreMatrixList = function(targets, windows=NULL, bin.num=NULL,
 
 	# ----------------------------------------------------------------- #
 	# checks whether the list argument contains only scoreMatrix objects
-	if(all(unlist(lapply(targets, class)) == 'scoreMatrix'))
+	if(all(unlist(lapply(targets, class)) == 'ScoreMatrix'))
 		return(new("ScoreMatrixList",targets))
 
 	# ----------------------------------------------------------------- #
@@ -114,7 +114,7 @@ ScoreMatrixList = function(targets, windows=NULL, bin.num=NULL,
            GRangesList, a list of GRanges objects')
 	}  
 
-	if(all(file.exists(targets)) & is.null(type))
+	if(!list.ind && all(file.exists(targets)) && is.null(type))
       stop('When providing a file, it is necessary to give the type of the file')
 
 	# gets the names for the resulting list

inst/doc/GenomationManual-knitr.Rnw

@@ -236,13 +236,12 @@ is used to represent results from multiple experiments.
 It can be in one of the three formats: a list of RleLists, a list of GRanges (or a GRangesList object), 
 or a character vector designating a set of .bam files.
 <<ScoreMatrixList, eval=FALSE, tidy=TRUE>>=
-library(genomationData)
 data(promoters)
 data(cpgi)
 data(cage)
 
 cage$tpm = NULL
-targets = list(cage=cage, cpgi=cpge)
+targets = list(cage=cage, cpgi=cpgi)
 sm = ScoreMatrixList(targets=targets, windows=promoters, bin.num=50)
 @