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A protein Quantitative Trait Locus toolkit

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.

Aspects involving data from ongoing project have been simplified to use files in pQTLtools/testswhich can be made public when appropriate.

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