removedSnpFemaleChrXhweControl: Hardy Weinberg Equilibrium test for chromosome X SNPs in...

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

Hardy Weinberg Equilibrium test for chromosome X SNPs in female controls.

Description

Hardy Weinberg Equilibrium test for SNPs on the chromosome X in female controls.

Usage

removedSnpFemaleChrXhweControl(
  plink,
  inputPrefix,
  pval = 1e-06,
  outputPvalFile,
  outputSNPfile,
  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.
pval	the p-value cutoff for controlling HWE test in female control subjects. Only chromosome X SNPs are considered. The default value is 0.000001.
outputPvalFile	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, one per line.
outputPrefix	the prefix of the output PLINK binary files.

Value

The output PLINK binary files after HWE test on chromosomal X in female controls.

Author(s)

Junfang Chen

See Also

removedSnpHWEauto

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"  
outputPvalFile <- "2_12_snpHwePvalfemaleXct.txt" 
outputSNPfile <- "2_12_snpRemovedHweFemaleXct.txt" 
outputPrefix <- "2_12_removedSnpHweFemaleX"
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpFemaleChrXhweControl(plink, inputPrefix, pval=0.000001,
##                                outputPvalFile, outputSNPfile, 
##                                outputPrefix)

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