manhattan: Produce a manhattan plot.

In CharlesJB/manhattan: Produce manhattan plot

Description

Produce a manhattan plot.

Usage

manhattan(gr_snps, title, pvalue = NULL, status = NULL, r2 = NULL,
  geno_ld = NULL, extra_ggplot2 = NULL)

Arguments

gr_snps	A GRanges object.
title	The title of the plot.
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)
r2	The name of the column to use for showing r2. Default: NULL.
geno_ld	The file *.geno.ld produced by 'vcftools' or a data.frame from the file loaded with read.table.
extra_ggplot2	Extra modifications to add to the graph. Must be valid ggplot2 expressions.

Value

corresponding to the input file table.

Examples

dataset <- load_dataset()

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