A collection of R scripts that might be useful for exploring and plotting GWAS results. Some are derived from scripts from Dr. Lars Fritsche, Dr. Wei Zhou, Dr. Sarah Graham.
The following R packages need to be installed for running these Rscripts:
optparse, data.table, RColorBrewer, plotrix, pwr, ggplot2
Frequency binned and thinned QQ plot. Also calculates median genomic control inflation factor, lambda. 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
| CHROM | POS | MAF | PVALUE |
|---|---|---|---|
| 1 | 1 | 0.05 | 0.99 |
| 2 | 2 | 0.15 | 0.1 |
| 3 | 3 | 0.5 | 0.25 |
Convert alelle count (AC) to minor allele count (MAC) in additional column titled MAC or custom name (--colName). Requires columns with AC and sample size (N) and an input and output file name.
Convert allele frequency (AF) to minor allele frequency (MAF) in additional column titled MAF or custom name (--colName). Requires columns with AF and an input and output file name.
Create scatterplots to compare values from two columns in a data frame. Print Pearson's correlation of the value sto standard out. Please check out the required/available Rscript parameters by using the following command:
Rscript comparisonPlot.R --help
Transform beta values from linear mixed model so they are comparable to beta values from logistic/linear regression. This implements work from Cook et al (doi:10.1038/ejhg.2016.150) and Lloyd-Jones et al (doi:10.1534/genetics.117.300360). Please check out the required/available Rscript parameters by using the following command:
Rscript transformBeta.r --help
Given a list of rsIDs for SNPs of interest, find SNPs in linkage disequlibrium (proxy SNPs) using NCBI LDproxy API request. Search a VCF to see if SNPs of interest of their proxies are present in the study of interest. rsID to coordinate conversion and vice versa is in development. Written in Python 2.7.14 with requests module version '2.18.4'.
python getLDproxy.py --help
Rscript QQplot.r \
--input ExampleGWAS.txt \
--prefix Example \
--maf MAF \
--pvalue PVALUE \
--maintitle 'An Example QQ plot'
Rscript ManhattanPlot.r
--input ExampleGWAS.txt \
--prefix Example \
--chr CHROM \
--pos POS \
--pvalue PVALUE \
--maintitle 'An Example Manhattan plot'
Rscript AFtoMAF.r
--input ExampleGWAS.txt \
--output Example_minor.txt \
--af A1Freq \
--colName MAF
Rscript ACtoMAC.r
--input ExampleGWAS.txt \
--output Example_minor.txt \
--ac AC \
--colName MAC
Rscript comparisonPlot.R
--input ExampleGWAS.txt \
--prefix Example_comparison \
--VAL1 p.value
--VAL2 Logreg.pval
--labdata1 "SAIGE" \
--labdata2 "HAIL" \
--title "Pvalue comparison in all variants" \
--negLog10 TRUE
Rscript transformBeta.R
--input ExampleGWAS.txt \
--prefix ExampleGWAS \
--numCase 1000 \
--numControl 4000 \
--pathToFunc shiny_lmor_func.R
Rscript Lambda.r
--input ExampleGWAS.txt \
--prefix ExampleGWAS \
--af A1Freq \
--pvalue Logreg.pval \
--minMAF 1e-6
python getLDproxy.py --in_rs rsID.txt \
--dbsnp_vcf All_20180423.vcf.gz \
--study_vcf study.vcf.gz