import_plink.pedmap: import_plink.pedmap

In geneHapR: Gene Haplotype Statistics, Phenotype Association and Visualization

import_plink.pedmap

Description

used for import regular p.link file stored in map and ped format

Usage

import_plink.pedmap(root = root,
                      sep_ped = "\t", sep_map = "\t",
                      pedfile = pedfile, mapfile = mapfile)

Arguments

root	The file name without suffix. This function only support p.link file format stored in "map" and "ped" format, the file names after removed suffix should be same with each other.
sep_ped	a character indicate the separation of ped file
sep_map	a character indicate the separation of map file
pedfile, mapfile	if root is missing then pedfile and mapfile are needed

Value

list, contains map information stored in data.frame and ped information stored in data.frame

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)

geneHapR documentation built on May 29, 2024, 11:59 a.m.