add_r2_from_vcftools: Add r2 values to GRanges object

In CharlesJB/manhattan: Produce manhattan plot

Description

This function will: 1) Find the best SNPs in gr_snps using the pvalue parameter. 2) Will extract relevant lines from geno_ld. 3) Create r2 vector.

Usage

add_r2_from_vcftools(geno_ld, gr_snps, pvalue = NULL, status = NULL)

Arguments

geno_ld	The file *.geno.ld produced by 'vcftools' or a data.frame from the file loaded with read.table.
gr_snps	A GRanges object.
pvalue	The name of the column to use as pvalue. Default: NULL (the first numerical metadata column will be used)
status	Name of the column for the SNP status (Genotype or Imputed). If value is NULL, all the SNPs will be used to find the best SNP, otherwise only SNPs with Genotyped value will be used. Default: NULL.

Value

A numeric vector corresponding to the pairwise LD of best SNP versus all the other SNPs.

CharlesJB/manhattan documentation built on May 6, 2019, 9:58 a.m.