removedMonoSnp: Exclude monomorphic SNPs

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

Exclude monomorphic SNPs

Description

Detect monomorphic SNPs from PLINK BIM file and exclude them if any.

Usage

removedMonoSnp(plink, inputPrefix, outputPrefix, outputSNPfile)

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.
outputPrefix	the prefix of the output PLINK binary files after removing monomorphic SNPs.
outputSNPfile	the output pure text file that stores the removed monomorphic SNPs, one per line, if any.

Value

The output PLINK binary files after removing monomorphic SNPs and a pure text file with removed monomorphic SNPs.

Author(s)

Junfang Chen

Examples

 
## In the current working directory
bedFile <- system.file("extdata", "alignedData.bed", package="Gimpute")
bimFile <- system.file("extdata", "alignedData.bim", package="Gimpute") 
famFile <- system.file("extdata", "alignedData.fam", package="Gimpute")
system(paste0("scp ", bedFile, " ."))   
system(paste0("scp ", bimFile, " ."))   
system(paste0("scp ", famFile, " ."))   
inputPrefix <- "alignedData"
outputPrefix <- "removedMonoSnp" 
outputSNPfile <- "monoSNP.txt"  
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedMonoSnp(plink, inputPrefix, outputPrefix, outputSNPfile)

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