Calculate ESTIMATE Scores — deconvo

Calculates stromal, immune, and ESTIMATE scores from gene expression.

Usage

deconvo_estimate(eset, project = NULL, platform = "affymetrix")

Arguments

eset: Gene expression matrix with gene symbols.
project: Optional project name. Default is `NULL`.
platform: Platform type: `"affymetrix"` or `"illumina"`. Default is `"affymetrix"`.

Value

Data frame with ESTIMATE scores. Columns suffixed with `_estimate`.

Author

Dongqiang Zeng

Examples

if (FALSE) { # \dontrun{
common_genes <- load_data("common_genes")
if (!is.null(common_genes)) {
  set.seed(123)
  sim_eset <- matrix(rnorm(nrow(common_genes) * 2), nrow(common_genes), 2)
  rownames(sim_eset) <- common_genes$GeneSymbol
  colnames(sim_eset) <- paste0("Sample", 1:2)
  result <- deconvo_estimate(sim_eset, project = "TCGA-STAD")
  if (!is.null(result)) head(result)
}
} # }