IntersectionNotStrict: Count reads overlapping genomic ranges

In jianhong/diffPeaks: Quantifying Differential Features

Description

Count reads overlapping a set of genimc features represented as genomic ranges. This function does not work for parallel.

Usage

IntersectionNotStrict(features, reads, ignore.strand = TRUE,
  inter.feature = FALSE)

Arguments

features	A object of GRanges representing the feature regions to be counted.
reads	An object that represents the data to be counted. See summarizeOverlaps. If reads are more than 1 bam files, it should be a vector of character with full path, otherwise current working directory is the default directory. For paired end reads,
ignore.strand	logical(1). ignore strand?
inter.feature	not used. This parameter is required by summarizeOverlaps.

Value

return a summarized experiment object with chromosome-level depth information for each input sample as metadata.

jianhong/diffPeaks documentation built on May 22, 2019, 12:37 p.m.