mxr_create_region_file: Create the Region File from the Clumps.
In roslen/mxr: A Package of GWAS Pipeline Building Blocks

Description Usage Arguments Details Value

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.)

1 2	mxr_create_region_file(genotype_prefix, reference_alleles = "", clumped_snps = "", out_prefix = "", verbose = FALSE)

`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)