removeNoGroupId: Remove samples without group information

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

Remove samples without group information

Description

Remove samples without group/outcome/phenotype information, which is coded as -9 in the PLINK .FAM file.

Usage

removeNoGroupId(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.

Value

The output PLINK binary files after removing samples without group information.

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_04_removedNoGroupId" 
## Not run: Requires an executable program PLINK, e.g.
## plink <- "/home/tools/plink"
## removeNoGroupId(plink, inputPrefix, outputPrefix)

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