removedMaleHetX: Remove male subjects with haploid heterozygous SNPs

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

Description

Determine the frequency of

Usage

removedMaleHetX(plink, inputPrefix, hhSubjCutOff, outputPrefix,
  outputFile_subjHetFreqAll, outputFile_subjHetFreqRetained,
  outputFile_SNPhhFreqAll)

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.
hhSubjCutOff	the cutoff for removing male subjects with haploid heterozygous SNPs on the chromosome X.
outputPrefix	the prefix of the output PLINK format files.
outputFile_subjHetFreqAll	the output pure text file that stores male subjects that have heterozygous SNPs with their frequency (if any), i.e. the number of .hh SNPs in this male.
outputFile_subjHetFreqRetained	the output pure text file that stores male subjects that have heterozygous SNPs with their frequency after 'improper' subject removal (if any).
outputFile_SNPhhFreqAll	the output pure text file that stores all 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.

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