manhattan_plot: Creates the Manhattan plot

In GWASinspector: Comprehensive and Easy to Use Quality Control of GWAS Results

Creates the Manhattan plot

Description

A function to generate Manhattan plots.

Usage

manhattan_plot(
  dataset,
  chr,
  pvalue,
  position,
  fileName,
  plot.title = "Manhattan Plot",
  plot.subtitle = "",
  p.threshold = 0.01,
  sig.threshold.log = -log10(5 * 10^-8),
  beta = NULL,
  std.error = NULL,
  check.columns = TRUE
)

Arguments

dataset	Data frame or data table containing the below columns
chr	Name of chromosome column
pvalue	Name of P-value column
position	Name of position column
fileName	Full name and path of file to be saved (file extension should be 'png'). e.g. “c:/users/researcher/study/man_plot.png”
plot.title	Title of the plot, default value is 'Manhattan plot'
plot.subtitle	Subtitle of the plot
p.threshold	Threshold for plotting variants (i.e. p-values > 0.01 will not be plotted). Setting a higher threshold will significantly increase plotting time
sig.threshold.log	The -log10 transformed significance threshold, used for plotting a threshold line (e.g. 8 = 10^-8)
beta	(optional) Name of the effect-size column
std.error	(optional) Name of the standard error column
check.columns	Whether to check input columns for invalid values

Value

Generates and saves a Manhattan plot for the provided data.

GWASinspector documentation built on Sept. 28, 2023, 1:06 a.m.