dot-mergePlinkData: Merge chunk-wise PLINK files

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

Merge chunk-wise PLINK files

Description

Merge all chunk-wise PLINK binary files into chromosome-wise PLINK binary files then assemble into a genome-wide PLINK binary file set.

Usage

.mergePlinkData(plink, chrs, prefix4eachChr, prefix4mergedPlink, nCore)

Arguments

plink	an executable program in either the current working directory or somewhere in the command path.
chrs	specifiy the chromosome codes to be merged.
prefix4eachChr	the prefix of the input chunk-wise PLINK files.
prefix4mergedPlink	the prefix of the final output PLINK binary files.
nCore	the number of cores used for computation.

Details

Create a file containing a list chunk-wise PLINK PED and MAP file names. The prefix of these files must already indicate in which chromosome they belong to and files from the same chromosome will be combined. Then all chromosomal PLINK files are assembled together into one whole genome PLINK binary file set.

Value

The merged genome-wide PLINK binary files.

Author(s)

Junfang Chen

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