gcComp {InPAS}R Documentation

Calculate weights for GC composition

Description

Calculate read weights for GC composition-based coverage correction

Usage

gcComp(genome, seqnames, window = 50, BPPARAM = NULL)

Arguments

genome

An object of BSgenome::BSgenome

seqnames

a character(n) vector, the chromosome/scaffolds' names in the same forms of seqnames in the BSgenome

window

size of a sliding window, which optimally is set to the read length

BPPARAM

an optional BiocParallel::BiocParallelParam instance determining the parallel back-end to be used during evaluation, or a list of BiocParallelParam instances, to be applied in sequence for nested calls to bplapply. It can be set to NULL or bpparam()

Value

A list of numeric vectors containing the weight (scaffold-level GC\ / GC\ chromosome/scaffold.

Author(s)

Jianhong Ou, Haibo Liu

References

Cheung et al. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res. 2011 Aug;39(15):e103.

Examples

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

## End(Not run)

[Package InPAS version 2.1.0 Index]