lbroseus / methylcc

R package to estimate the cell composition in DNA methylation samples in microarray or sequencing platforms using any reference cell-type specific data

Extending methylCC to handle any reference cell types

This is a package to estimate the cell composition of bulk DNA methylation measured on any platform technology (e.g. Illumina 450K microarray, whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS)) using reference cell-type-specific methylation data.

Updates from the original version

29/01/2021: version 2.0.0

• Added the option to use already processed methylation data (eg: normalized beta values).
• New function find_dmrs_custom() for finding Differentially Methylated Regions (DMRs) from custom reference-cell-type-specific methylation data (esp: in tissues other than Whole Blood)

Installing methylCC

The R-package methylCC can be installed from Github using the R package devtools:

To install the tinkered version of methylCC from Github:

library(devtools)
install_github("lbroseus/methylCC")

After installation, the package can be loaded into R.

library(methylCC)

Installing the original version of methylCC

To install the original version of methylCC from Github:

library(devtools)
install_github("stephaniehicks/methylCC")

Citation

Hicks SC, Irizarry RA. (2019). Genome Biology 20, 261. https://doi.org/10.1186/s13059-019-1827-8

Authors

• Stephanie C. Hicks
• Rafael A. Irizarry