setHeteroHaploMissing: Set haploid heterozygous SNPs as missing

In transbioZI/Gimpute: Gimpute: An efficient genetic data processing and imputation pipeline

Set haploid heterozygous SNPs as missing

Description

Set all heterozygous alleles of chromosome X SNPs in male as missing.

Usage

setHeteroHaploMissing(plink, inputPrefix, outputPrefix)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the input PLINK binary files.
outputPrefix	the prefix of the output PLINK binary files.

Value

The output PLINK binary files after setting haploid heterozygous SNPs as missing.

Author(s)

Junfang Chen

Examples

## In the current working directory
bedFile <- system.file("extdata", "genoUpdatedData.bed", package="Gimpute")
bimFile <- system.file("extdata", "genoUpdatedData.bim", package="Gimpute") 
famFile <- system.file("extdata", "genoUpdatedData.fam", package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))  
inputPrefix <- "genoUpdatedData" 
outputPrefix <- "2_03_setHeteroHaploMissing" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## setHeteroHaploMissing(plink, inputPrefix, outputPrefix)

transbioZI/Gimpute documentation built on April 10, 2022, 4:20 a.m.