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 2.2.0 Index]