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’ (https://github.com/phenoscanner/). 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