ReadCountMatrix: Compute read counts over genomic intervals for multiple bam...

In benja0x40/Tightrope: ChIP-seq normalization according to background reads density

Description

Compute read counts over genomic intervals for multiple bam files

Usage

ReadCountMatrix(bam.files, grg, paired, names = NULL, maxgap = -1L,
  minoverlap = 0L, type = "any", ignore.strand = TRUE, ...)

Arguments

bam.files	character vector containing paths to the bam files (mapped reads).
grg	a GRanges object defining the considered genomic intervals.
paired	logical vector, must be set to TRUE for files with paired-end reads and to FALSE for files with single-end reads. For conciseness, a single logical value can be provided when all bam files are consistent with this value.
names	user provided column names for the resulting count matrix. When omitted, the bam file names are used.
maxgap	See ?findOverlaps in the IRanges package for a description of these arguments.
minoverlap	See ?findOverlaps in the IRanges package for a description of these arguments.
type	See ?findOverlaps in the IRanges package for a description of these arguments.
ignore.strand	When set to TRUE, the strand information is ignored in the overlap calculations.
...	optional arguments forwarded to readGAlignments or readGAlignmentPairs.

Value

ReadCountMatrix returns a read counts matrix where rows correspond to the provided genomic intervals and columns to the provided bam files.

See Also

DitherCounts, NormalizeCountMatrix, PlotCountDistributions

benja0x40/Tightrope documentation built on May 24, 2019, 1:35 a.m.