removedSnpMissPostImp: Remove SNPs after post imputation

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

Remove SNPs after post imputation

Description

Remove SNPs which have a non missing value for less than a predefined number of instances.

Usage

removedSnpMissPostImp(
  plink,
  inputPrefix,
  missCutoff,
  outRemovedSNPfile,
  outRetainSNPfile,
  outputPrefix
)

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.
missCutoff	the cutoff of the least number of instances for a SNP that is not missing. The default is 20.
outRemovedSNPfile	the output file of SNPs with pre-defined missing values that are removed.
outRetainSNPfile	the output file of SNPs that are retained.
outputPrefix	the prefix of the PLINK binary files.

Value

The PLINK binary files after post imputation quality control and a pure text file contains SNPs with pre-defined missing values.

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 <- "removedSnpMissPostImp" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpMissPostImp(plink, inputPrefix, missCutoff=20, 
##                       outRemovedSNPfile, outRetainSNPfile, outputPrefix)
## 

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