manhattan: Produce a manhattan plot.

Description Usage Arguments Value Examples

View source: R/manhattan.R

Description

Produce a manhattan plot.

Usage

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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

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dataset <- load_dataset()

CharlesJB/manhattan documentation built on June 1, 2017, 11:12 p.m.