removedSnpFemaleChrXmiss: remove chromosome X SNPs in females

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

remove chromosome X SNPs in females

Description

Remove SNPs on the chromosome X with a pre-defined cutoff for missingness in females.

Usage

removedSnpFemaleChrXmiss(
  plink,
  femaleChrXmissCutoff,
  inputPrefix,
  outputPrefix
)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
femaleChrXmissCutoff	the cutoff of the missingness in female chromosome X 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.

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, " ."))  
femaleChrXmissCutoff <- 0.05
inputPrefix <- "genoUpdatedData"  
outputPrefix <- "2_10_removedSnpFemaleChrXmiss" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpFemaleChrXmiss(plink, femaleChrXmissCutoff, 
##                          inputPrefix, outputPrefix)

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