gt.format: Format genotype for BayEnv and BayPass

In rCNV: Detect Copy Number Variants from SNPs Data

Format genotype for BayEnv and BayPass

Description

This function generates necessary genotype count formats for BayEnv and BayPass with a subset of SNPs

Usage

gt.format(
  gt,
  info,
  format = c("benv", "bpass"),
  snp.subset = NULL,
  parallel = FALSE
)

Arguments

gt	multi-vector. an imported data.frame of genotypes or genotype data frame generated by hetTgen or path to GT.FORMAT file generated from VCFTools
info	a data frame containing sample and population information. It must have “sample” and “population” columns
format	character. output format i.e., for BayPass or BayEnv
snp.subset	numerical. number of randomly selected subsets of SNPs. default = NULL
parallel	logical. whether to parallelize the process

Value

Returns a list with formatted genotype data: $bayenv - snps in horizontal format - for BayEnv (two lines per snp); $baypass - vertical format - for BayPass (two column per snp); $sub.bp - subsets snps for BayPass $sub.be - subsets of snps for BayEnv

Author(s)

Piyal Karunarathne

Examples

## Not run: vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
het.table<-hetTgen(vcf,"GT")
info<-unique(substr(colnames(het.table)[-c(1:3)],1,8))
GT<-gt.format(het.table,info)
## End(Not run)

rCNV documentation built on Sept. 30, 2024, 9:39 a.m.