removedSnpFemaleChrXhweAll: Hardy weinberg equilibrium test for chromosome X SNPs in...

Description Usage Arguments Value Author(s)

Description

Hardy weinberg equilibrium test for chromosome X SNPs in all female subjects. If only control data, then it's the same as the test with all female control subjects.

Usage

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removedSnpFemaleChrXhweAll(plink, inputPrefix, pval, outputFile_pVal,
  outputSNPfile, outputPrefix)

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.

pval

the p-value cutoff for controlling HWE test in female subjects. Only chromosome X SNPs are tested here.

outputFile_pVal

the output pure text file that stores chromosome X SNPs and their sorted HWE p-values.

outputSNPfile

the output pure text file that stores the removed SNPs.

outputPrefix

the prefix of the output PLINK format files.

Value

The output PLINK format files.

Author(s)

Junfang Chen <junfang.chen3@gmail.com>


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