calculate_sig_score_integration: Calculate Signature Score Using Integration Method

In IOBR: Immune Oncology Biological Research

Calculate Signature Score Using Integration Method

Description

Computes signature scores using PCA, z-score, and ssGSEA methods combined.

Usage

calculate_sig_score_integration(
  pdata = NULL,
  eset,
  signature,
  mini_gene_count = 2,
  column_of_sample = "ID",
  adjust_eset = FALSE,
  parallel.size = 1L
)

Arguments

pdata	Data frame with phenotype data. If 'NULL', created from 'eset' column names.
eset	Expression matrix (genes as rows, samples as columns).
signature	List of gene signatures.
mini_gene_count	Minimum genes required per signature. Default is 3.
column_of_sample	Column in 'pdata' with sample IDs. Default is '"ID"'.
adjust_eset	Logical: remove problematic features. Default is 'FALSE'.
parallel.size	Number of parallel workers. Default is 1.

Value

Tibble with signature scores from all three methods.

Author(s)

Dongqiang Zeng

Examples

set.seed(123)
eset <- matrix(rnorm(1000), nrow = 100, ncol = 10)
rownames(eset) <- paste0("Gene", 1:100)
colnames(eset) <- paste0("Sample", 1:10)
signature <- list(
  Signature1 = paste0("Gene", 1:15),
  Signature2 = paste0("Gene", 16:30)
)

result <- calculate_sig_score_integration(eset = eset, signature = signature)

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