manhattan: Creates a manhattan plot using ggplot2 and returns the plot...

In SelectionPredisposed/qqman2: Plots for GWAS

Description

Creates a manhattan plot using ggplot2 and returns the plot object.

Usage

manhattan(x, snp = "SNP", chr = "CHR", bp = "BP", p = "P",
  maf = "MAF", typed = NA, annotation = NA, thresholdLow = 5,
  thresholdHigh = -log10(5e-08), thresholdLowColor = "blue",
  thresholdHighColor = "red", mafColor = "black", build = "b37",
  title = Sys.time())

Arguments

x	A data frame with result data
snp	SNP column in data frame
chr	Chromosome column in data frame
p	P-value column in data frame
maf	MAF column in data frame
typed	the column in the data frame indicating whether the markers are genotyped or imputed (ignored if NA)
annotation	a vector of annotation (ignored if NA)
thresholdLow	the low threshold value (log10)
thresholdHigh	the high threshold value (log10)
thresholdLowColor	the color of the low threshold
thresholdHighColor	the color of the high threshold
mafColor	the color of the low maf values
build	What build to use for plotting ('b37' or 'b38', default is 'b37')
title	Title of plot (date by default, ignored if NA)
pb	SNP position column in data frame

Value

A manhattan plot (ggplot2 object)

SelectionPredisposed/qqman2 documentation built on May 21, 2019, 1:41 a.m.