readExpSet {spliceSites} | R Documentation |
Opens multiple BAM-files and reads aligns for selected gene for each file. Number of alignes is counted.
readExpSet(bam, idx, val="nAligns", phenoData, expData)
bam |
Vector of BAM-files |
idx |
Vector of index files (optional) |
val |
"gptm", "rpmg" or "nAligns". Value type which is written to ExpressionSet matrix (nAligns = read count). |
phenoData |
|
expData |
|
ExpressionSet
Wolfgang Kaisers
# A) Names of BAM-files bam <- character(2) bam[1] <- system.file("extdata", "rna_fem.bam", package="spliceSites") bam[2] <- system.file("extdata", "rna_mal.bam", package="spliceSites") # B) Experiment Profile prof <- data.frame(gender=c("f", "m")) meta <- data.frame(labelDescription=names(prof), row.names=names(prof)) pd <- new("AnnotatedDataFrame", data=prof, varMetadata=meta) # C) Read ExpressionSet es <- readExpSet(bam, phenoData=pd) # D) Annotate ExpressionSet ucf <- system.file("extdata", "uc_small_junc.RData", package="spliceSites") juc <- loadGenome(ucf) ann <- annotate(es, juc) phenoData(es) <- ann