gcContents {InPAS} | R Documentation

## 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)

[Package InPAS version 2.2.0 Index]