plotPCA4plink.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/genotypeQC.R
\name{plotPCA4plink}
\alias{plotPCA4plink}
\title{Population outlier detection}
\usage{
plotPCA4plink(
  gcta,
  inputPrefix,
  nThread = 20,
  outputPC4subjFile,
  outputPCplotFile
)
}
\arguments{
\item{gcta}{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{nThread}{the number of threads used for computation. 
The default is 20.}

\item{outputPC4subjFile}{the pure text file that stores all the subject IDs 
and their corresponding eigenvalues of the first two principle components.}

\item{outputPCplotFile}{the plot file for visualizing the first two 
principle components of all investigated subjects.}
}
\value{
The output pure text file and plot file for storing first two 
principle components of study subjects.
}
\description{
Principle component analysis (PCA) on the genotype data is performed 
to detect population outliers, and the first two PCs 
are plotted for the visualization.
}
\details{
Before population outlier detection, it's better to perform QC 
on the genotype data. 
Only autosomal genotypes are used for principle component analysis.
}
\examples{
 
## In the current working directory
bedFile <- system.file("extdata", "QCdata.bed", package="Gimpute")
bimFile <- system.file("extdata", "QCdata.bim", package="Gimpute") 
famFile <- system.file("extdata", "QCdata.fam", package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))  
inputPrefix <- "QCdata" 
outputPC4subjFile <- "2_13_eigenvalAfterQC.txt"
outputPCplotFile <- "2_13_eigenvalAfterQC.png" ## png format
## Not run: Requires an executable program GCTA, e.g.
## gcta <- "/home/tools/gcta64"
## plotPCA4plink(gcta, inputPrefix, nThread=20, 
##               outputPC4subjFile, outputPrefix)
}
\author{
Junfang Chen
}