Calculate Signature Score Using Z-Score Method — calculate_sig_score

Computes signature scores using z-score transformation.

Usage

calculate_sig_score_zscore(
  pdata = NULL,
  eset,
  signature,
  mini_gene_count = 3,
  column_of_sample = "ID",
  adjust_eset = FALSE
)

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`.

Value

Tibble with signature scores.

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_zscore(eset = eset, signature = signature)
#> ℹ Calculating signature scores using z-score method
#> ℹ Log2 transformation not necessary (data appears to already be log-scaled)
#> ℹ Calculating scores for 2 signature(s)