darneson / methylresolver

Robust method for deconvolving bulk tissue methylation data using least trimmed squares (LTS) regression

MethylResolver

Contents

• Overview
• Repo Contents
• System Requirements
• Installation Guide
• Demo
• License
• Issues
• Version

Overview

MethylResolver is an R package to conduct robust deconvolution of bulk tissue methylation profiles using a reference signature. A reference signature of 11 leukocyte cell types is provided. Additionally, tumor purity and tumor purity-adjusted cell type fractions can be estimated without a reference of the tumor using a Random Forest regression model trained on concensus tumor purity estimates (CPE) of TCGA samples.

MethylResolver was developed and is maintained by Douglas Arneson at UCLA.

Repo Contents

• R: R package code.
• man: package manual for help in R session.
• data: data used in the tutorial, the RF model, and the signature matrix.

System Requirements

Hardware Requirements

The MethylResolver package requires only a standard computer with Rstudio installed.

Software Requirements

OS Requirements

The package has tested on Mac OSX operating systems. The package has been tested on the following systems:

Linux:
Mac OSX: macOS Mojave 10.14.6
Windows:

The R package should be compatible with Windows, Mac, and Linux operating systems.

Before setting up the MethylResolver package, users should have R version 3.4.0 or higher.

Installation Guide

Stable Release

MethylResolver is available from github:

install.packages('devtools')
devtools::install_github(repo = 'darneson/MethylResolver')
library(MethylResolver)

Typical install times are 1-2 minutes.

Demo

Examples

For demos of the functions, please check out the examples built into the package. They can be accessed as follows:

require(MethylResolver)

# Deconvolution with default signature and calculating absolute fractions with default RF model:
MethylResolver(methylMix = MethylMix)

# Deconvolution with default signature and calculating absolute fractions with default RF model while 
# specifying a particular alpha value:
MethylResolver(methylMix = MethylMix, alpha = 0.5)

# Deconvolution with default signature and only calculating relative fractions:
MethylResolver(methylMix = MethylMix, absolute = FALSE)

# Specify your own signature matrix and RF model for calculating absolute fractions:
MethylResolver(methylMix = MethylMix, methylSig = MethylSig, purityModel = RFmodel)

Typical run times for the examples are ~10 seconds.

Also, please look at the built in help for descriptions of the parameters using: ?MethylResolver.

Version History

February 20, 2019:

• Version 0.1.0 released (initial release)