mxr_create_region_file: Create the Region File from the Clumps.

Description Usage Arguments Details Value

Description

mxr_create_region_file creates the region file that will be used to extract the corresponding information from SNPs stored in the SNP reference file (that contains the reference alleles collated from processing the VCF files.)

Usage

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mxr_create_region_file(genotype_prefix, reference_alleles = "",
  clumped_snps = "", out_prefix = "", verbose = FALSE)

Arguments

genotype_prefix

The fullpath and prefix of the bim/bed/fam plink files.

reference_alleles

The genome-wide list of reference allele for each SNP. It has three mandatory columns: chr, bp, Ref_allele. Chr column may have values like "chr01"..."chr12", bp are just the base pair positions of the SNPs, and the Ref_allele column is formatted as "Ref=<nuc>".

clumped_snps

These are contained in the file outputted by mxr_extract_clumped_snps(). That function needs to be run first prior to this.

out_prefix

Path and prefix of the output files.

verbose

(Optional) Show verbose output. (DEFAULT=FALSE)

Details

The output of this file will be used in annotating the GWAS results.

Value

TRUE if the PLINK run completed successfully. FALSE, otherwise.


roslen/mxr documentation built on May 27, 2019, 11:32 p.m.