removedSnpHWEauto.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/genotypeQC.R
\name{removedSnpHWEauto}
\alias{removedSnpHWEauto}
\title{Hardy Weinberg Equilibrium test for autosomal SNPs}
\usage{
removedSnpHWEauto(
  groupLabel,
  plink,
  inputPrefix,
  pval = 1e-06,
  outputPvalFile,
  outputSNPfile,
  outputPrefix
)
}
\arguments{
\item{groupLabel}{a string value indicating the outcome label: "control",
or, "case" or "caseControl" for both existing groups. For more details, see 
\code{\link{getGroupLabel}}.}

\item{plink}{an executable program in either the current working directory 
or somewhere in the command path.}

\item{inputPrefix}{the prefix of the input PLINK binary files.}

\item{pval}{the p-value cutoff for controlling HWE test in either control or 
case subjects. Only autosomal SNPs are considered. The default value is
0.000001.}

\item{outputPvalFile}{the output pure text file that stores autosomal SNPs
and their sorted HWE p-values.}

\item{outputSNPfile}{the output pure text file that stores the removed SNPs, 
one per line.}

\item{outputPrefix}{the prefix of the output PLINK binary files.}
}
\value{
The output PLINK binary files after HWE test on the autosome.
}
\description{
Remove autosomal SNPs deviating from Hardy Weinberg Equilibrium (HWE).
}
\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, " ."))  
groupLabel <- "control"
inputPrefix <- "genoUpdatedData" ## Specify the input PLINK file prefix 
outputPvalFile <- "2_11_snpHwePvalAuto.txt"
outputSNPfile <- "2_11_snpRemovedHweAuto.txt" 
outputPrefix <- "2_11_removedSnpHweAuto" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpHWEauto(groupLabel, plink, inputPrefix, pval=0.000001,
##                   outputPvalFile, outputSNPfile, outputPrefix)
}
\seealso{
\code{\link{removedSnpFemaleChrXhweControl}}, 
\code{\link{getGroupLabel}}.
}
\author{
Junfang Chen
}