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EPIC package

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Description

Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data. It is based on reference gene expression profiles for the main non-malignant cell types and it predicts the proportion of these cells and of the remaining “other cells” (that are mostly cancer cells) for which no reference profile is given.

This method is described in the publication from Racle et al., 2017 available at https://elifesciences.org/articles/26476.

EPIC is also available as a web application: http://epic.gfellerlab.org.

Usage

The main function in this package is EPIC. It needs as input a matrix of the TPM (or RPKM) gene expression from the samples for which to estimate cell proportions. One can also define the reference cells to use

# library(EPIC) ## If the package isn't loaded (or use EPIC::EPIC and so on).
out <- EPIC(bulk = bulkSamplesMatrix)
out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList)

out is a list containing the various mRNA and cell fractions in each sample as well as some data.frame of the goodness of fit.

Values of mRNA per cell and signature genes to use can also be changed:

out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList, mRNA_cell = mRNA_cell_vector, sigGenes = sigGenes_vector)
out <- EPIC(bulk = bulkSamplesMatrix, reference = referenceCellsList, mRNA_cell_sub = mRNA_cell_sub_vector)

Various other options are available and are well documented in the help pages from EPIC:

?EPIC::EPIC
?EPIC::EPIC.package

Installation

install.packages("devtools")
devtools::install_github("GfellerLab/EPIC", build_vignettes=TRUE)

Web application

EPIC is also available as a web application: http://epic.gfellerlab.org.

Python wrapper

A pyhton wrapper has been written by Stephen C. Van Nostrand from MIT and is available at https://github.com/scvannost/epicpy.

License

EPIC can be used freely by academic groups for non-commercial purposes. The product is provided free of charge, and, therefore, on an “as is” basis, without warranty of any kind. Please read the file “LICENSE” for details.

If you plan to use EPIC (version 1.1) in any for-profit application, you are required to obtain a separate license. To do so, please contact Nadette Bulgin (nbulgin@lcr.org) at the Ludwig Institute for Cancer Research Ltd.

Contact information

Julien Racle (julien.racle@unil.ch), and David Gfeller (david.gfeller@unil.ch).

FAQ

Which proportions returned by EPIC should I use?
What do the “other cells” represent?
I receive an error message “attempt to set ‘colnames’ on an object with less than two dimensions”. What can I do?
Is there some caution to consider about the cellFractions and mRNA_cell values?
I receive a warning message that “the optimization didn’t fully converge for some samples”. What does it mean?
Who should I contact in case of a technical or other issue?