removedMendelErr: Check Mendel errors for family-based data

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

Check Mendel errors for family-based data

Description

Exclude subjects and/or genetic variants (SNPs) based on Mendel errors in the family data (trio/duo).

Usage

removedMendelErr(
  plink,
  inputPrefix,
  cutoffSubject = 0.05,
  cutoffSNP = 0.1,
  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.
cutoffSubject	the cutoff determines that families (subjects) with more than the predefined cutoff of Mendel errors by considering all SNPs will be removed. The default is 0.05.
cutoffSNP	the cutoff indicates that SNPs with more than the predefined cutoff of Mendel error rate will be excluded (i.e. based on the number of trios/duos). The default is 0.1.
outputPrefix	the prefix of the output PLINK binary files.

Details

Do make sure that all your family relationships are correct in your input data before applying this function. The input PLINK data should have complete sex and group/outcome information. By default, trios and duos are both considered. If no family information is given at all (only founders), then this function will not remove any subjects or variants but give the warning showing that no duos or trios are present.

Value

The output PLINK binary files.

Author(s)

Junfang Chen

Examples

## In the current working directory
bedFile <- system.file("extdata", "dataWithFamChr21.bed", package="Gimpute")
bimFile <- system.file("extdata", "dataWithFamChr21.bim", package="Gimpute") 
famFile <- system.file("extdata", "dataWithFamChr21.fam", package="Gimpute")
system(paste0("scp ", bedFile, bimFile, famFile, " ."))  
inputPrefix <- "dataWithFamChr21" 
outputPrefix <- "removedMendelErr" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removedMendelErr(plink, inputPrefix, 
##                  cutoffSubject, cutoffSNP, outputPrefix)

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