IntersectionNotStrict: Count reads overlapping genomic ranges
In jianhong/NADfinder: Call wide peaks for sequencing data

IntersectionNotStrict

R Documentation

Count reads overlapping genomic ranges

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

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

`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.