calculate_sig_score: Calculate Signature Score

In IOBR: Immune Oncology Biological Research

Calculate Signature Score

Description

Main interface for calculating signature scores from gene expression data. Supports PCA, z-score, ssGSEA, and integration methods.

Usage

calculate_sig_score(
  pdata = NULL,
  eset,
  signature = NULL,
  method = c("pca", "ssgsea", "zscore", "integration"),
  mini_gene_count = 3,
  column_of_sample = "ID",
  print_gene_proportion = FALSE,
  print_filtered_signatures = FALSE,
  adjust_eset = FALSE,
  parallel.size = 1L,
  ...
)

Arguments

pdata	Phenotype data. If 'NULL', created from 'eset' column names.
eset	Expression matrix (CPM, TPM, RPKM, FPKM, etc.).
signature	List of gene signatures. Can also be a character string naming a built-in signature collection (e.g., '"signature_collection"', '"signature_tme"', '"go_bp"', '"kegg"', '"hallmark"').
method	Scoring method: '"pca"', '"ssgsea"', '"zscore"', or '"integration"'. Default is '"pca"'.
mini_gene_count	Minimum genes required per signature. Default is 3 (or 5 for ssGSEA).
column_of_sample	Column with sample IDs in 'pdata'. Default is '"ID"'.
print_gene_proportion	Logical: print gene coverage. Default is 'FALSE'.
print_filtered_signatures	Logical: print filtered signatures. Default is 'FALSE'.
adjust_eset	Logical: clean problematic features. Default is 'FALSE'.
parallel.size	Parallel workers for ssGSEA. Default is 1.
...	Additional arguments passed to specific methods.

Value

Tibble with phenotype data and signature scores.

Author(s)

Dongqiang Zeng

References

1. Hänzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis. BMC Bioinformatics. 2013;14:7.

2. Mariathasan S, et al. TGF\beta attenuates tumour response to PD-L1 blockade. Nature. 2018;554:544-548.

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", 1:10),
  Signature2 = paste0("Gene", 11:20)
)

result <- calculate_sig_score(eset = eset, signature = signature, method = "pca")

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