qqplotter: Quantile-quantile plot for observed vs. expected p-values
Description
qqplotter returns a pdf file containing the
QQ-plot for a given set of p-values
Usage
qqplotter(p_values = NULL, res.file = NULL, p.num.col = NULL, sep = " ", out.file = "QQplot.pdf", title = "")
Arguments
p_values
A vector or a column in a data-set
containing p-values to plot. This is an alternative to
file.
res.file
File name of the file containing
p-values to retrieve. This alternative does not require
loading the results and is an alternative to the
p_values parameter.
p.num.col
Number indicating which column of the
file contains p-values. Specify only if you are
using the file option.
sep
File separator to be used when reading
file. Default is white space.
title
Title to appear on the plot.
out.file
File name for the output plot.
Value
The output will be a pdf file containing the QQplot.
Details
The function is useful for comparing expected and
observed distributions of statistics arising from
genome-wide testing. Two different types of input are
allowed:
- an object such as vector or
data-frame column, containing p-values;
- a file name
and the column number for retrieving p-values from file.
Note that separator is set to white space, can be changed
accordingly if needed. The special character "*" is
allowed for selecting more than on file (e.g. in case
there is one file for each chromosome) but the p-values
column position must be the same for all files.