getFeatureCounts: get the read counts for a supplied set of genomic features

In girafe: Genome Intervals and Read Alignments for Functional Exploration

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

girafe documentation built on Nov. 8, 2020, 4:56 p.m.