gwasTools

gwasTools

A collection of R scripts that might be useful to plot GWAS results.

The following R pakages need to be installed for running these Rscripts:

optparse, data.table, RColorBrewer, plotrix, pwr, Map2NCBI, basicPlotteR, devtools devtools::install_github('JosephCrispell/basicPlotteR')

QQ Plot

Frequency binned and thinned QQ plot.

Please check out the required/available Rscript parameters by using the following command

Rscript QQplot.r --help

Manhattan Plot

Fast Manhattan plot script. Please check out the required/available Rscript parameters by using the following command

Rscript ManhattanPlot.r --help

80% Power Plot

80% Power plots based on Cohen's effect size calculation for proportions as implemented in the 'pwr' R package

Rscript PowerPlot.r --help

Minimal/example Input format for QQ and Manhattan plots

CHROM	POS	MAF	PVALUE
1	1	0.05	0.99
2	2	0.15	0.1
3	3	0.5	0.25

Examples (run from command line):

Rscript QQplot.r 
--input ExampleGWAS.txt 
--prefix Example 
--maf MAF 
--pvalue PVALUE 
--maintitle 'An Example QQ plot'


# GWAS results from http://csg.sph.umich.edu/abecasis/public/amd2015/Fritsche_2015_AdvancedAMD.txt.gz
Rscript ManhattanPlot.r 
--input Fritsche_2015_AdvancedAMD.txt.gz 
--prefix Example 
--chr Chrom 
--pos Pos 
--pvalue GC.Pvalue 
--coltop T 
--maintitle 'Age-related macular degeneration (Fritsche et al. 2016)' 
--threads 8


Rscript PowerPlot.r 
--prefix Example 
--cases 500,1000,5000 
--controls 1000,2000,10000 
--minMAF 0.001 
--alpha 5E-8