removedSnpMissDiff: Remove SNPs with difference in SNP missingness between cases...

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

Remove SNPs with difference in SNP missingness between cases and controls.

Description

Remove SNPs with difference in SNP missingness between cases and controls. To test for differential call rates between cases and controls for each SNP

Usage

removedSnpMissDiff(
  plink,
  inputPrefix,
  snpMissDifCutOff,
  outputPrefix,
  groupLabel
)

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.
snpMissDifCutOff	the cutoff of the difference in missingness between cases and controls.
outputPrefix	the prefix of the output PLINK binary files.
groupLabel	a string value indicating the outcome label: "control", or, "case" or "caseControl" for both existing groups. For more details, see getGroupLabel.

Details

Only if both case-control groups exist in the input genotype data, differential SNPs are removed.

Value

The output PLINK binary files.

Author(s)

Junfang Chen

See Also

getGroupLabel.

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, " ."))  
inputPrefix <- "genoUpdatedData" 
snpMissDifCutOff <- 0.02
outputPrefix <- "2_09_removedSnpMissDiff" 
groupLabel <- "control"
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedSnpMissDiff(plink, inputPrefix, snpMissDifCutOff, 
##                    outputPrefix, groupLabel)

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