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 1.46.0 Index]