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It seeds collection of data and utilities for pQTL analysis. At this early stage, the repository contains 1. Articles linking functions for cis/trans classification, 2d Manhattan plots, 2d/3d-plotly plots, forest plots among others available from gap,; 2. Query on genes, regions, and SNPs via PhenoScanner,, adding functionality to check for replication across platforms; 3. Downstream analysis such as colocalization, pQTL-Mendelian Randomization via TwoSampleMR,, linkage through UniProt IDs to other resources; 4. Bioconductor notes and a showcase of snakemake workflow.


Available functions are listed in the following table.

get.prop.below.LLODLimit of detection analysis
import_eQTLCatalogueImport eQTL Catalogue
import_OpenGWASImport OpenGWAS
make_ExpressionSetA call to ExpressionSet class
novelty_checkLocus novelty check
run_colocColocalisation analysis
MR analysis 
pqtlMRBidirectional pQTL-MR analysis
qtl_lookupQTL lookup
run_TwoSampleMRA generic wrapper for TwoSampleMR analysis
PhenoScanner Utilities 
genequeriesphenoscanner genequeries in batches
regionqueriesphenoscanner regionqueries in batches
snpqueriesphenoscanner snpqueries in batches
UniProt API 
uniprot2idsUniProt ID to others
Functions in gap 
gap::METAL_forestplotForest plots from metal analysis
gap::ci2msEffect size and standard error from confidence interval
gap::cis.vs.trans.classificationa cis/trans classifier
gap::circos.cis.vs.trans.plotcircos plot of cis/trans classification
gap::circos.mhtplotcircos Manhattan plot with gene annotation
gap::circos.mhtplot2Another circos Manhattan plot
gap::csCredible set
gap::get_b_seGet b and se from AF, n, and z
gap::get_pve_seGet pve and its standard error from n, z
gap::get_sdyGet sd(y) from AF, n, b, se
gap::mrMendelian randomization analysis
gap::invnormalInverse normal transformation
gap::log10plog10(p) for a standard normal deviate
gap::log10pvaluelog10(p) for a P value including its scientific format
gap::logplog(p) for a normal deviate
gap::mhtplot.truncTruncated Manhattan plot
gap::miamiplot2Miami plot
gap::mr_forestplotMendelian Randomization forest plot
gap::pvalueP value for a normal deviate
gap::qtlClassifierA QTL cis/trans classifier
gap::qtl2dplot2D QTL plot
gap::qtl2dplotly2D QTL plotly
gap::qtl3dplotly3D QTL plotly


Vignettes on package usage:


Jing Hua Zhao in collaboration with other colleagues