splitXchr: Split chromosome X into pseudoautosomal region and...

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

Split chromosome X into pseudoautosomal region and non-pseudoautosomal region.

Description

Split chromosome X into pseudoautosomal region and non-pseudoautosomal region, if chromosome X data is available.

Usage

splitXchr(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

Genomic coordinate system is on genome build hg19.

Value

The output PLINK binary files after splitting chromosome X into pseudoautosomal region and non-pseudoautosomal region.

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_10_splitXchr" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removeSampID(plink, inputPrefix, outputPrefix)

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