IntersectionNotStrict {NADfinder} | R Documentation

## Count reads overlapping genomic ranges

### 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.

[Package NADfinder version 1.16.0 Index]