QQ plots
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 Quesenberry and Hales (1980) 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.
References
Quesenberry CP, Hales C (1980). “Concentration bands for uniformity plots.” J Statist Comput Simul, 11(1), 41-53. doi:10.1080/00949658008810388 .
Author
Bram Prins, https://github.com/bpprins/turboqq.
Examples
if (FALSE) {
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()
}