removeOutlierByPCs: Remove population outliers by principle components

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

Description

This function decides if one would remove population outliers or not. If the outliers are necessary to be removed then one uses the eigenvalues from the first principle component as a criterion for finding out the outliers by defining a proper cutoff.

Usage

removeOutlierByPCs(plink, gcta, inputPrefix, cutoff, cutoffSign,
  inputPC4subjFile, outputPC4outlierFile, outputPCplotFile, 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.
cutoff	the cutoff that would distinguish the outliers from ordinary population. If it is null, then no outliers or not necessary to remove outliers. If it has only a value, then one also has to define the cutoffSign as below. If it has two values, then one doesn't have to define the cutoffSign.
cutoffSign	the cutoff sign: 'greater' or 'smaller' that would determine if the outliers should be greater or smaller than the cutoff value. if the cutoff score has two values, then no need to define the cutoffSign.
inputPC4subjFile	the pure text file that stores all the subject IDs after QC and their corresponding eigenvalues of the first two principle components, if any.
outputPC4outlierFile	the pure text file that stores the outlier IDs and their corresponding eigenvalues of the first two principle components, if any.
outputPCplotFile	the plot file for visualizing the first two principle components of all subjects without population outliers, if any.
outputPrefix	the prefix of the output PLINK format files..
outputSNPs	the output pure text file that stores the removed monomorphic SNPs.

Value

The output PLINK format files after outlier removal. The output pure text file (if any) for storing removed outlier IDs and their corresponding PCs. The plot file (if any) for visualizing the first two principle components after outlier removal.

Author(s)

Junfang Chen <[e-mail]>

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