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Calculate Signature Score

Source: R/calculate_sig_score.R
calculate_sig_score.Rd

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.

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.

Author

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", 1:10),
  Signature2 = paste0("Gene", 11:20)
)
result <- calculate_sig_score(eset = eset, signature = signature, method = "pca")
#> ℹ Calculating signature scores using PCA method
#> ℹ Log2 transformation not necessary (data appears to already be log-scaled)
#> ℹ Calculating scores for 2 signature(s)