turboqq: QQ plots
In jinghuazhao/pQTLtools: A Protein Quantitative Trait Locus Toolkit

turboqq

R Documentation

QQ plots

Description

QQ plots

Usage

turboqq(input_data_path, plot_title, plot_resolution = 1800)

Arguments

`input_data_path`	Path of the input association data.
`plot_title`	Plot title to be displayed on top of the plot.
`plot_resolution`	a fixed number of points (pixels) to be plotted vertically and horizontally.

Details

The method uses the kth order statistic from a sample of n i.i.d. U(0,1) statistics has a Beta(k,n+1-k) distribution as in \insertCitequesenberry80;textualpQTLtools and Coded by Weale M, Price T. https://sites.google.com/site/mikeweale/software

Input association data file / input_data_path

Define path of the input association data. The input data needs to be a file that has:

Spaces as field separators.
One header line.
Option I. (no extreme p-values present): 3 columns, being chromosome, position, pvalue in order, column names are not important. Option II. (extreme p-values present): 5 columns, being chromosome, position, pvalue, beta, se in order, column names are not important.

Plot title / plot_title

Define plot title which will be displayed on top of the plot.

Resolution of plot / plot_resolution

Define a fixed number of points (pixels) to be plotted vertically and horizontally.

Value

No direct return value. The script generates QQ plots as output.

Author(s)

Bram Prins, https://github.com/bpprins/turboqq.

References

\insertAllCited

Examples

## Not run: 
png('test_qq.png', height = 1800, width = 1800, pointsize = 12, res = 450)
par(mar = c(4, 4, 3, 1))
require(gap.datasets)
test <- mhtdata[c('chr','pos','p')]
write.table(test,file='test.txt',row.names=FALSE,quote=FALSE)
input_data_path <- 'test.txt'
plot_title <- 'gap.datasets example'
turboqq(input_data_path, plot_title)
dev.off()

## End(Not run)

jinghuazhao/pQTLtools documentation built on Dec. 16, 2024, 3:44 p.m.