ClrCNV: multicopy detection for WGS — allele.info.WGS • rCNV

This function is catered for detecting multicopy regions from whole genome sequences (WGS) using Likelihood Ratios

Usage

allele.info.WGS(
  ad,
  gt,
  fis = NULL,
  vcf = NULL,
  parallel = FALSE,
  numCores = NULL,
  ...
)

Arguments

ad: allele depth table generated with hetTgen
gt: genotype table generated with hetTgen
fis: global inbreeding coefficient calculated with h.zygosity
vcf: if fis is not provided, vcf file imported using readVCF
parallel: logical. to parallelize over multiple cores
numCores: numeric. if parallel TRUE, number of cores to use; if NULL, use all cores
...: other arguments passed to makeCluster

Value

Returns a data frame with likelihood ratios per SNP and duplication status

Author

Qiujie Zhou, Pascal Milesi, Piyal Karunarathne

Examples

if (FALSE) { # \dontrun{
vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
ad<-hetTgen(vcf,"AD")
gt<-hetTgen(vcf,"GT")
hz<-h.zygosity(vcf,verbose=FALSE)
Fis<-mean(hz$Fis,na.rm = TRUE)
AI_WGS<-allele.info.WGS(ad,gt,Fis=Fis)} # }