removedSnpHetX: Remove heterozygous SNPs in haploid male chromosome X

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

Description

In principle, one has to remove all heterozygous SNPs of chromosome X in males. However, too many SNPs might be removed in some data sets. We want to accept a small percentage of such SNPs in the data set so that we do not lose too much SNPs.

Usage

removedSnpHetX(plink, inputPrefix, hhCutOff, outputPrefix,
  outputFile_SNPhhFreqAll, outputFile_SNPhhFreqRetained)

Arguments

plink	an executable PLINK program in either the current working directory or somewhere in the command path.
inputPrefix	the prefix of the input PLINK format files.
hhCutOff	the cutoff for removing male haploid heterozygous SNPs on the chromosome X.
outputPrefix	the prefix of the output PLINK format files.
outputFile_SNPhhFreqAll	the output pure text file that stores all heterozygous SNPs with their frequency (the number of males for this SNP), if any.
outputFile_SNPhhFreqRetained	the output pure text file that stores retained heterozygous SNPs with their frequency (the number of males for this SNP), if any.

Value

The output PLINK format files and two pure text files (if any) with heterozygous SNPs and their respective frequency.

Author(s)

Junfang Chen <[e-mail]>

Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.