dot-gwasvcf_to_coloc_rsid: Prepare gwasvcf files for coloc. This method will extract...

In jwr-git/mrpipeline: Implements a Ready-for-Use Mendelian Randomisation Pipeline

Prepare gwasvcf files for coloc. This method will extract SNPs from one file using one chrompos and then look up those SNPs in the other file – this is to ensure coloc can be conducted upon two datasets of different genomic builds without the need of liftover.

Description

Prepare gwasvcf files for coloc. This method will extract SNPs from one file using one chrompos and then look up those SNPs in the other file – this is to ensure coloc can be conducted upon two datasets of different genomic builds without the need of liftover.

Usage

.gwasvcf_to_coloc_rsid(
  vcf1,
  vcf2,
  chrompos,
  type1 = NULL,
  type2 = NULL,
  build1 = "GRCh37",
  build2 = "GRCh37",
  verbose = TRUE
)

Arguments

vcf1	VCF object or path to vcf file
vcf2	VCF object or path to vcf file
chrompos	Character of the format chr:pos1-pos2

Value

list of coloc-ready data, or NA if failed

jwr-git/mrpipeline documentation built on Oct. 2, 2022, 3:41 p.m.