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

<img src="/Example_QQ.png" height="480">

Manhattan Plot

Fast Manhattan plot script with adaptive data thinning for handling large GWAS datasets efficiently. The script intelligently reduces data points while preserving significant associations.

New Thinning Features:

• --thinning_mode: Choose between "adaptive" (default), "random", or disable with --disable_thinning T
• --thinning_aggressiveness: Control thinning intensity (0.1=aggressive, 1.0=normal, 2.0=less aggressive)
• --thinning_sig_threshold: Significance threshold for keeping variants (-log10P, default=6)

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

Rscript ManhattanPlot.r --help

<img src="/Example_Manhattan.png" height="480">

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

<img src="/Example_PowerAnalysis.png" height="480">

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

# Example with custom thinning for large datasets
Rscript ManhattanPlot.r \
--input large_gwas_results.txt \
--prefix LargeGWAS \
--thinning_aggressiveness 0.5 \
--maintitle 'Large GWAS with aggressive thinning'


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