Chemoproteomics Data Analysis

Authors: Yuting Xu, Andy Liaw, Huijun Wang

Copyright© 2019 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA.

Last updated: 07/03/2019

Requirements

• R (>= 3.4.0)
• R packages: drc, truncnorm, magrittr, dplyr, knitr, ggplot2, gridExtra, reshape2, tidyr, limma

Install

• Option 1) Install from github

if('rCPDMS' %in% installed.packages()){remove.packages('rCPDMS')}
# install.packages("devtools")
devtools::install_github("Merck/rCPDMS")

• Option 2) Install from R-package source file rCPDMS_0.1.3.tar.gz in this repository

if('rCPDMS' %in% installed.packages()){remove.packages('rCPDMS')}
install.packages("rCPDMS_0.1.3.tar.gz", repos = NULL, type = "source")

Usage

Follow the scripts in demo/demo_CPDMS.R to set parameters for model fitting. Example datasets are included in folder data_raw.

Workflows

• Pull down
• Cellular Thermal Shift Assay (CETSA)
• Iso-Thermal Dose Response (2dCETSA)

Notes

The example code in miscellaneous/processMaxquantProtein.R demonstrates how to take a maxquant protein output (protein.txt) and the mapping file (MappingTemplaete.csv) to generate input data file for rCPDMS package.