A protein Quantitative Trait Locus toolkit

It collects data and utilities for pQTL analysis, including 1. Protein GWAS facilities such as Manhattan/QQ/LocusZoom.js plots, novelty/consequence checking; 2. Articles linking functions for cis/trans classification, pQTL-gene plot, 2d/3d-plotly plots, forest plots among others available from gap, https://cran.r-project.org/package=gap, as well as colocalization, pQTL-Mendelian Randomization via TwoSampleMR. https://mrcieu.github.io/TwoSampleMR/; 3. Query on genes, regions, and SNPs via PhenoScanner, http://www.phenoscanner.medschl.cam.ac.uk/. 4. Mapping of UniProt IDs to other resources; 5. Showcases of Bioconductor, https://github.com/bioconductor, and snakemake, https://github.com/snakemake.

Installation

The latest version of pQTLtools can be installed as usual:

1. Install from R

if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")
remotes::install_github("jinghuazhao/pQTLtools")

2. Install from GitHub repository

git clone https://github.com/jinghuazhao/pQTLtools
R CMD INSTALL pQTLtools

Dependencies are detailed in the DECRIPTION file of the package at GitHub.

A summary of functions

This can be seen from R with

library(help=pQTLtools)

or

library(pQTLtools)
?pQTLtools