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

eset_stad <- load_data("eset_stad")
anno_grch38 <- load_data("anno_grch38")
eset <- anno_eset(eset = eset_stad, annotation = anno_grch38, probe = "id")
#> ℹ Row number of original eset: 60483
#> ✔ 100% of probes in expression set were annotated
#> ℹ Found 2293 duplicate symbols, using "mean" method
#> ℹ Row number after filtering duplicated gene symbol: 50181
estimate_result <- deconvo_estimate(eset, project = "TCGA-STAD")
#> ℹ Running ESTIMATE
#> [1] "Merged dataset includes 10148 genes (264 mismatched)."
#> [1] "1 gene set: StromalSignature  overlap= 138"
#> [1] "2 gene set: ImmuneSignature  overlap= 140"