QQ plots

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.

Value

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

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 quesenberry80;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:

1. Spaces as field separators.

2. One header line.

3. 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

Author

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

Examples

if (FALSE) { # \dontrun{
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()
} # }