removedYMtSnp: Remove SNPs on the chromosome Y and mitochondrial DNA

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

Remove SNPs on the chromosome Y and mitochondrial DNA

Description

Remove SNPs on the chromosome Y and mitochondrial DNA.

Usage

removedYMtSnp(plink, inputPrefix, 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.
outputPrefix	the prefix of the output PLINK binary files.

Details

Note that if chromosome Y and mitochondrial DNA are available, they must be coded as 24 and 26, respectively.

Value

The output PLINK binary files after removing SNPs on the chromosome Y and mitochondrial DNA.

Author(s)

Junfang Chen

Examples

## In the current working directory
bedFile <- system.file("extdata", "controlData.bed", package="Gimpute")
bimFile <- system.file("extdata", "controlData.bim", package="Gimpute") 
famFile <- system.file("extdata", "controlData.fam", package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))  
inputPrefix <- "controlData" ## Specify the input PLINK file prefix 
outputPrefix <- "1_11_removedYMtSnp" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedYMtSnp(plink, inputPrefix, outputPrefix)

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