manhattan.qtl: make manhattan plots of MatrixEQTL results

In matthiasheinig/eQTLpipeline: A package to facilitate the full pipeline of cis eQTL analysis

Description

convenience function to create ggplot2 manhattan plots of MatrixEQTL objects

Usage

manhattan.qtl(me, build = "b37", snp.pos = NULL, trait = NULL,
  vcf = NULL, build.names = NULL)

Arguments

me	MatrixEQTL results as list or data.frame
build	genome build to use, options: "b37", "b38", "custom" (default "b37")
snp.pos	data.frame with SNP annotations if not in me, SNP by cols: colnames(snp.pos) <- c("snps", "chr", "pos")
trait	character vector of gene/trait names to plot
vcf	vcf file to extract SNP annotations from (default NULL)
build.names	names for colums with annotations for custom build, order: chr, length (default NULL)

Value

ggplot2 object (list) with the plot

Author(s)

Ines Assum (2019-03-21)

matthiasheinig/eQTLpipeline documentation built on May 21, 2019, 1:16 p.m.