removedInstFhet: Remove subjects with abnormal autosomal heterozygosity...

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

Remove subjects with abnormal autosomal heterozygosity deviation

Description

Remove subjects with great autosomal heterozygosity deviation.

Usage

removedInstFhet(plink, Fhet, inputPrefix, outputPrefix)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
Fhet	the cutoff of the autosomal heterozygosity deviation.
inputPrefix	the prefix of the input PLINK binary files.
outputPrefix	the prefix of the output PLINK binary files.

Details

If the cutoff of the autosomal heterozygosity deviation is set to be greater than 0.2, i.e. |Fhet| >= 0.2, then this analysis will automatically skip haploid markers (male X and Y chromosome markers).

Value

The output PLINK binary files after removing subjects with great autosomal heterozygosity deviation.

Author(s)

Junfang Chen

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, " ."))  
Fhet <- 0.2
inputPrefix <- "genoUpdatedData" 
outputPrefix <- "2_06_removedInstFhet" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedInstFhet(plink, Fhet, inputPrefix, outputPrefix)

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