manhattan_plot {GWASinspector}

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,
  useHQ = 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

useHQ

Whether to only plot HQ variants

Value

Generates and saves a Manhattan plot for the provided data.