Format genotype for BayEnv and BayPass

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

Piyal Karunarathne

Examples

if (FALSE) vcf.file.path <- paste0(path.package("rCNV"), "/example.raw.vcf.gz")
vcf <- readVCF(vcf.file.path=vcf.file.path)
#> Error in eval(expr, envir, enclos): object 'vcf.file.path' not found
het.table<-hetTgen(vcf,"GT")
#> Error in eval(expr, envir, enclos): object 'vcf' not found
info<-unique(substr(colnames(het.table)[-c(1:3)],1,8))
#> Error in eval(expr, envir, enclos): object 'het.table' not found
GT<-gt.format(het.table,info) # \dontrun{}
#> Error in eval(expr, envir, enclos): object 'het.table' not found