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, https://github.com/jinghuazhao/R/tree/master/gap; 2. Query on genes, regions, and SNPs via PhenoScanner, http://www.phenoscanner.medschl.cam.ac.uk/, adding functionality to check for replication across platforms; 3. Downstream analysis such as colocalization, pQTL-Mendelian Randomization via TwoSampleMR, https://github.com/MRCIEU/TwoSampleMR, linkage through UniProt IDs to other resources; 4. Bioconductor notes and a showcase of snakemake workflow.
Details
Available functions are listed in the following table.
| Objects | Description |
| eQTL/GWAS | |
get.prop.below.LLOD | Limit of detection analysis |
import_eQTLCatalogue | Import eQTL Catalogue |
import_OpenGWAS | Import OpenGWAS |
make_ExpressionSet | A call to ExpressionSet class |
novelty_check | Locus novelty check |
run_coloc | Colocalisation analysis |
| MR analysis | |
pqtlMR | Bidirectional pQTL-MR analysis |
qtl_lookup | QTL lookup |
run_TwoSampleMR | A generic wrapper for TwoSampleMR analysis |
| PhenoScanner Utilities | |
genequeries | phenoscanner genequeries in batches |
regionqueries | phenoscanner regionqueries in batches |
snpqueries | phenoscanner snpqueries in batches |
| UniProt API | |
uniprot2ids | UniProt ID to others |
| Functions in gap | |
gap::METAL_forestplot | Forest plots from metal analysis |
gap::ci2ms | Effect size and standard error from confidence interval |
gap::cis.vs.trans.classification | a cis/trans classifier |
gap::circos.cis.vs.trans.plot | circos plot of cis/trans classification |
gap::circos.mhtplot | circos Manhattan plot with gene annotation |
gap::circos.mhtplot2 | Another circos Manhattan plot |
gap::cs | Credible set |
gap::get_b_se | Get b and se from AF, n, and z |
gap::get_pve_se | Get pve and its standard error from n, z |
gap::get_sdy | Get sd(y) from AF, n, b, se |
gap::mr | Mendelian randomization analysis |
gap::invnormal | Inverse normal transformation |
gap::log10p | log10(p) for a standard normal deviate |
gap::log10pvalue | log10(p) for a P value including its scientific format |
gap::logp | log(p) for a normal deviate |
gap::mhtplot.trunc | Truncated Manhattan plot |
gap::miamiplot2 | Miami plot |
gap::mr_forestplot | Mendelian Randomization forest plot |
gap::pvalue | P value for a normal deviate |
gap::qtlClassifier | A QTL cis/trans classifier |
gap::qtl2dplot | 2D QTL plot |
gap::qtl2dplotly | 2D QTL plotly |
gap::qtl3dplotly | 3D QTL plotly |
Usage
Vignettes on package usage:
An Overview of pQTLtools.
vignette("pQTLtools").Bioconductor Notes.
vignette("bioconductor").ExpressionSet usage.
vignette("es").snakemake showcases.
vignette("snakemake").SCALLOP-INF scripts.
vignette("SCALLOP-INF").