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')
Frequency binned and thinned QQ plot.
Please check out the required/available Rscript parameters by using the following command
Rscript QQplot.r --help
Fast Manhattan plot script. Please check out the required/available Rscript parameters by using the following command
Rscript ManhattanPlot.r --help
80% Power plots based on Cohen's effect size calculation for proportions as implemented in the 'pwr' R package
Rscript PowerPlot.r --help
| CHROM | POS | MAF | PVALUE |
|---|---|---|---|
| 1 | 1 | 0.05 | 0.99 |
| 2 | 2 | 0.15 | 0.1 |
| 3 | 3 | 0.5 | 0.25 |
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