View source: R/00.get_GCandMappability.R
gcComp | R Documentation |
Calculate read weights for GC composition-based coverage correction
gcComp(genome, seqnames, window = 50, future.chunk.size = 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 |
future.chunk.size |
The average number of elements per future ("chunk"). If Inf, then all elements are processed in a single future. If NULL, then argument future.scheduling = 1 is used by default. Users can set future.chunk.size = total number of elements/number of cores set for the backend. See the future.apply package for details. |
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)
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