tabulateReads: tabulate counts of alignments occurring in specified genomic...

In vjcitn/leeBamViews: leeBamViews -- multiple yeast RNAseq samples excerpted from Lee 2009

Description

tabulate counts of alignments occurring in specified genomic regions

Usage

tabulateReads(bv, strandmarker=NULL, as.GRanges=FALSE, applier=lapply)

Arguments

bv	BamViews-class instance
strandmarker	character atom: ‘+’ or ‘-’; if missing, ignore strand
as.GRanges	logical directive to return a GRanges instance instead of a matrix
applier	lapply-like function; if unspecified and multicore is attached will use mclapply

Details

readGAlignments is the basic engine for this task

Value

annotated matrix with start, end, and samples as rows, regions as columns, and read counts as cell entries

Author(s)

VJ Carey <[e-mail]>

Examples

example(bs1)
#
# counts in a partition
#
myrn = GRanges(IRanges(start=seq(861250, 862750, 100), width=100),
    seqnames="Scchr13", strand="+")

values(myrn)$name = paste("til", 1:length(myrn), sep=".")
bamRanges(bs1) = myrn
tabulateReads(bs1, "+")
#
# a related computation based on countBam
lapply(bamPaths(bs1)[1:2], function(x) 
    countBam(x,  param=ScanBamParam(which=bamRanges(bs1))))

vjcitn/leeBamViews documentation built on Dec. 23, 2019, 7:37 p.m.