formatConvertGtool: Convert IMPUTE2 format files into PLINK format

Description Usage Arguments Value Author(s)

Description

Convert all chunks of IMPUTE2 format files into PLINK format using GTOOL.

Usage

1
2
formatConvertGtool(gtool, chrs, prefixChunk, phaseDIR, imputedDIR,
  prefix4plinkEachChr, suffix4imputed, postImputeDIR, nCore)

Arguments

gtool

an executable GTOOL program in either the current working directory or somewhere in the command path.

chrs

specifiy the chromosomes for conversion

prefixChunk

the prefix of the chunk files for each chromosome, along with the proper location directory.

phaseDIR

the directory where pre-phased files are located.

imputedDIR

the directory where the imputated files are located.

prefix4plinkEachChr

the prefix of the input IMPUTE2 files and also the output PLINK files for each chunk.

suffix4imputed

the suffix of the IMPUTE2 format file that stores the imputed value.

postImputeDIR

the directory where converted PLINK files will be located.

nCore

the number of cores used for computation.

Value

The converted PLINK format files for each chunk.

Author(s)

Junfang Chen <junfang.chen3@gmail.com>


Junfang/Gimpute documentation built on May 17, 2019, 10:11 p.m.