gcContents: helper function to calculate chromosome/scaffold level GC...

In jianhong/InPAS: Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

helper function to calculate chromosome/scaffold level GC content

Description

helper function to calculate chromosome/scaffold level GC content

Usage

gcContents(genome, seqname, nonATCGExclude = TRUE)

Arguments

genome	an object of BSgenome::BSgenome
seqname	a character(1) vector, the chromosome/scaffold's name
nonATCGExclude	a logical(1) vector, whether nucleotides other than A, T, C, and G should be excluded when GC content is calculated

Value

a numeric(1) vector, containing the chromosome/scaffold -specific GC content in the range of 0 to 1

Author(s)

Haibo Liu

Examples

## Not run: 
library(BSgenome.Mmusculus.UCSC.mm10)
genome <- BSgenome.Mmusculus.UCSC.mm10
InPAS:::gcContents(genome, "chr1")

## End(Not run)

jianhong/InPAS documentation built on Oct. 27, 2023, 2:13 p.m.