plink.pedmap2hap {geneHapR}

plink.pedmap2hap

Description

convert p.link format data into hapResult

Usage

plink.pedmap2hap(
  p.link,
  hapPrefix = "H",
  pad = 3,
  hetero_remove = TRUE,
  na_drop = TRUE
)

Arguments

p.link

list contains p.link information

hapPrefix

prefix of haplotype names

pad

The number length in haplotype names should be extend to.

hetero_remove

whether remove accessions contains hyb-sites

na_drop

whether drop accessions contains missing data ("N", NA)

Value

object of hapSummary class

Examples

   pedfile <- system.file("extdata",
                          "snp3kvars-CHR8-25947258-25951166-plink.ped",
                          package = "geneHapR")
   mapfile <- system.file("extdata",
                          "snp3kvars-CHR8-25947258-25951166-plink.map",
                          package = "geneHapR")
   p.link <- import_plink.pedmap(pedfile = pedfile, mapfile = mapfile,
                                 sep_map = "\t", sep_ped = "\t")
   p.link <- filter_plink.pedmap(p.link, mode = "POS",
                                 Chr = "chr08", start = 25948004,
                                 end = 25949944)
   hapResult <- plink.pedmap2hap(p.link, hapPrefix = "H",
                                 hetero_remove = TRUE,
                                 na_drop = TRUE)