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.
- R:
Rpackage code. - man: package manual for help in R session.
- data: data used in the tutorial, the RF model, and the signature matrix.
The MethylResolver package requires only a standard computer with Rstudio installed.
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.
MethylResolver is available from github:
install.packages('devtools')
devtools::install_github(repo = 'omnideconv/MethylResolver')
library(MethylResolver)Typical install times are 1-2 minutes.
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.
February 20, 2019:
- Version 0.1.0 released (initial release)