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https://github.com/darneson/MethylResolver
Robust method for deconvolving bulk tissue methylation data using least trimmed squares (LTS) regression
https://github.com/darneson/MethylResolver
Last synced: 17 days ago
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Robust method for deconvolving bulk tissue methylation data using least trimmed squares (LTS) regression
- Host: GitHub
- URL: https://github.com/darneson/MethylResolver
- Owner: darneson
- License: gpl-3.0
- Created: 2019-02-19T21:09:10.000Z (over 5 years ago)
- Default Branch: master
- Last Pushed: 2020-03-10T19:00:29.000Z (over 4 years ago)
- Last Synced: 2024-02-28T21:31:30.016Z (4 months ago)
- Language: R
- Size: 7.86 MB
- Stars: 5
- Watchers: 2
- Forks: 3
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Lists
- awesome-deconvolution - MethylResolver - 020-01146-2)); tags: methylation; dna_methylation; dnam; epigenetics; r (Methods)
README
# MethylResolver
[](https://travis-ci.org/darneson/MethylResolver)
[](http://hits.dwyl.com/darneson/MethylResolver)
[](https://www.gnu.org/licenses/gpl-3.0)
## Contents
- [Overview](#overview)
- [Repo Contents](#repo-contents)
- [System Requirements](#system-requirements)
- [Installation Guide](#installation-guide)
- [Demo](#demo)
- [License](./LICENSE)
- [Issues](https://github.com/darneson/MethylResolver/issues)
- [Version](#version-history)
# 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): `R` package code.
- [man](./man): package manual for help in R session.
- [data](./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:
```r
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)