readPlinkMendel: Read PLINK

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Read PLINK

Description

Read output files from the PLINK software used with the --mendel option. For potentially large files ("lmendel" and "mendel"), the fread function from the data.table package is used as it is faster than read.table.

Usage

readPlinkMendel(prefix, suffix = "", verbose = 1)

Arguments

prefix	prefix of the file to read (e.g. "~/work/output_plink")
suffix	suffix of the file to read fmendel: one row per parental pair imendel: one row per individual per parental pair lmendel: one row per variant (SNP) mendel: one row per error (Mendelian violation)
verbose	verbosity level (0/1)

Value

data frame

Author(s)

Timothee Flutre

Examples

## Not run: ## assuming properly-formatted data, launch PLINK via a system call
cmd <- "plink --mendel --bed input.bed --bim input.bim --fam input.fam --out output"
system(cmd)

pl.mend <- readPlinkMendel(prefix="output", suffix="mendel")
str(pl.mend)

pl.imend <- readPlinkMendel(prefix="output", suffix="imendel")
head(pl.imend[order(pl.imend$N, decreasing=TRUE),])

## End(Not run)

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.