removedSnpMiss: Remove SNPs with missing values

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

Remove SNPs with missing values

Description

Remove SNPs with missingness of greater than a certain threshold.

Usage

removedSnpMiss(plink, snpMissCutOff, inputPrefix, outputPrefix)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
snpMissCutOff	the cutoff of the missingness for removing SNPs.
inputPrefix	the prefix of the input PLINK binary files.
outputPrefix	the prefix of the output PLINK binary files.

Value

The output PLINK binary files after removing SNPs with pre-defined missing values.

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, " ."))  
snpMissCutOff <- 0.05
inputPrefix <- "genoUpdatedData" 
outputPrefix <- "2_04_removedSnpMissPre" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpMiss(plink, snpMissCutOff, inputPrefix, outputPrefix)

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