The deconvR package provides a collection of functions designed for
analyzing deconvolution of the bulk sample(s) using an atlas of
reference signature profiles and a user-selected model (non-negative
least squares,quadratic programming, support vector regression, or
robust linear regression). Users can directly use their reference atlas
or, create an expended version of their reference atlas using
findSignatures. Additionnaly, they can also use the reference atlas
provided within the package, which contains cell-type specific
methylation values. Another option is to simulate bulk signatures of
bulk samples using simulateCellMix. And finally, we included
BSmeth2Probe function along with the Illumina Methylation EPIC B5 Manifest
probe IDs, to be used to map methylation data to respective probe IDs.
The deconvR package can be installed from Bioconductor:
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("deconvR")You can also install the development version of deconvR directly from Github:
remotes::install_github("BIMSBbioinfo/deconvR")User who wish to expand their own reference atlas can use
findSignatures function. atlas is the signature matrix to be
extended and samples the new data to be added to the signature matrix.
atlas and samples are compliant with the function requirements.
After providing appropriate atlas format, users can create samples
using simulateCellMix function. You can get more information about
deconvR from here.