gcComp {InPAS} | R Documentation |
Calculate read weights for GC composition-based coverage correction
gcComp(genome, seqnames, window = 50, BPPARAM = NULL)
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() |
A list of numeric vectors containing the weight (scaffold-level GC\ / GC\ chromosome/scaffold.
Jianhong Ou, Haibo Liu
Cheung et al. Systematic bias in high-throughput sequencing data and its correction by BEADS. Nucleic Acids Res. 2011 Aug;39(15):e103.
## Not run: library(BSgenome.Mmusculus.UCSC.mm10) genome <- BSgenome.Mmusculus.UCSC.mm10 InPAS:::gcComp(genome, "chr1") ## End(Not run)