getFeatureCounts {girafe} | R Documentation

## get the read counts for a supplied set of genomic features

### Description

get the read counts for a supplied set of genomic features

### Usage

    getFeatureCounts(AI, FG, nameColumn = "Name", fractionIncluded = 1,
    returnType = "AlignedGenomeIntervals", mem.friendly = FALSE)

### Arguments

`AI` | `AlignedGenomeIntervals` object
`FG` | `Genome\_intervals` objects of genomic features
`nameColumn` | character indicating which column of the object `FG` holds the identifiers of the genomic features; is used to assess the number of genomic copies per feature
`fractionIncluded` | double; which fraction of an interval needs to be included in a feature in order to count for the feature
`returnType` | one of `AlignedGenomeIntervals` or `integer`
`mem.friendly` | logical; passed on to `fracOverlap` function, determines if overlap should be computed chromosome-wise, optionally distributed over several CPUs (with package `parallel`)

### Value

depends on argument `returnType`: one of `AlignedGenomeIntervals` or a named `integer`

### Author(s)

Joern Toedling

### See Also

`fracOverlap`

[Package girafe version 1.38.0 Index]