chunk4eachChr: Chunk each chromosome into multiple segments

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

Chunk each chromosome into multiple segments

Description

Chunk each chromosome genotyping data into multiple segments by a predefined window size.

Usage

chunk4eachChr(inputPrefix, outputPrefix, chrs, windowSize = 3e+06)

Arguments

inputPrefix	the prefix of the input PLINK .bim file for each chromosome, without the chromosome codes.
outputPrefix	the prefix of the output pure text files that keep all the chunks for each chromosome separately.
chrs	specifiy the chromosome codes for chunking.
windowSize	the window size of each chunk. The default value is 3000000.

Value

The output pure text files include all the chunks for each chromosome separately.

Author(s)

Junfang Chen

Examples

 
## In the current working directory
bimFile <- system.file("extdata", "gwas_data_chr23.bim", package="Gimpute") 
system(paste0("scp ", bimFile, " ."))    
inputPrefix <- "gwas_data_chr"
outputPrefix <- "chunks_chr"
chrs <- 23
print(chrs)   
chunk4eachChr(inputPrefix, outputPrefix, chrs, windowSize=3000000)

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