executePlinkMAF: Execute PLINK to Calculate Minor Allele Frequencies (MAF)

This function executes PLINK to calculate minor allele frequencies (MAF) for a given dataset. It sets up the necessary PLINK environment, runs the PLINK command, and returns the MAF results as a DataFrame. Intermediate files generated by PLINK are cleaned up after execution.

Usage

executePlinkMAF(DataDir, ResultDir, finput)

Arguments

DataDir

Character. Directory containing the input PLINK files (.bed, .bim, .fam).

ResultDir

Character. Directory to store the output files generated by PLINK.

finput

Character. Base name of the PLINK input files (without extensions).

Value

DataFrame containing the minor allele frequency (MAF) results.

Examples

DataDir <- GXwasR:::GXwasR_data()
ResultDir <- tempdir()
finput <- "GXwasR_example"
maf_data <- executePlinkMAF(DataDir, ResultDir, finput)