Calculate Immunophenoscore (IPS)

Calculates immune phenotype scores from gene expression data.

Usage

deconvo_ips(eset, project = NULL, plot = FALSE)

Arguments

eset

Gene expression matrix.

project

Optional project name. Default is `NULL`.

plot

Logical: generate visualization. Default is `FALSE`.

Value

Data frame with IPS scores. Columns suffixed with `_IPS`.

Author

Dongqiang Zeng

Examples

eset_stad <- load_data("eset_stad")
#> ℹ Loading cached data: "eset_stad"
anno_grch38 <- load_data("anno_grch38")
#> ℹ Loading cached 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
# \donttest{
ips_result <- deconvo_ips(eset = eset, project = "TCGA-STAD")
#> ℹ Running IPS calculation
#> ℹ Trying mirror 1/4: <https://github.com>
#> ✔ Download complete: "ips_gene_set"
# }