IPS_calculation: Calculate Immunophenoscore (IPS)

In IOBR: Immune Oncology Biological Research

Calculate Immunophenoscore (IPS)

Description

Calculates Immunophenoscore (IPS) from gene expression data. IPS is a composite score measuring immunophenotype based on four major categories: MHC molecules, immunomodulators, effector cells, and suppressor cells.

Usage

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

Arguments

eset	Gene expression matrix with official human gene symbols (HGNC) as rownames. Expression values should be log2(TPM+1) or will be transformed if max value > 100.
project	Character string for project identifier. Default is NULL.
plot	Logical. Whether to generate immunophenogram plots. Default is FALSE.

Value

Data frame containing:

MHC

MHC molecules score

EC

Effector cells score

SC

Suppressor cells score

CP

Checkpoints/Immunomodulators score

AZ

Aggregate score (sum of MHC, CP, EC, SC)

IPS

Immunophenoscore (0-10 scale)

Examples

## Not run: 
example_genes <- c(
  "HLA-A", "HLA-B", "HLA-C", "CD274", "PDCD1", "CTLA4",
  "CD8A", "CD8B", "GZMB", "PRF1", "FOXP3", "IL10"
)
sim_eset <- as.data.frame(matrix(
  rnorm(length(example_genes) * 5, mean = 5, sd = 2),
  nrow = length(example_genes), ncol = 5
))
rownames(sim_eset) <- example_genes
colnames(sim_eset) <- paste0("Sample", 1:5)
ips_result <- IPS_calculation(eset = sim_eset, project = "Example", plot = FALSE)
if (!is.null(ips_result)) head(ips_result)

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.