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Deconvolve Immune Microenvironment Using EPIC

Source: R/deconvo_tme.R
deconvo_epic.Rd

Estimates immune cell fractions using EPIC algorithm.

Usage

deconvo_epic(eset, project = NULL, tumor = TRUE)

Arguments

eset

Gene expression matrix with genes as row names.

project

Optional project name. Default is `NULL`.

tumor

Logical indicating tumor (`TRUE`) or normal (`FALSE`) samples.

Value

Data frame with EPIC cell fraction estimates. Columns suffixed with `_EPIC`.

Author

Dongqiang Zeng

Examples

if (FALSE) { # \dontrun{
TRef <- load_data("TRef")
if (!is.null(TRef)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(nrow(TRef$refProfiles) * 2), nrow(TRef$refProfiles), 2)
  rownames(sim_eset) <- rownames(TRef$refProfiles)
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_epic(eset = sim_eset, project = "Example", tumor = TRUE)
  if (!is.null(result)) head(result)
}
} # }