Map study factors to TCGA meta-programs — map_factors_to

For each study NMF factor, scores it against each TCGA meta-program by computing the mean NES of the meta-program's Hallmarks in that factor. The meta-program with the highest mean NES is the best match. If Bagaev MFP annotations are available (either embedded in the loaded meta-program object or in inst/extdata/bagaev_factor_annotations.RData), a mfp_label column is appended to the output.

Usage

map_factors_to_metaprograms(
  gsea_study,
  cancer_type,
  mp_file = NULL,
  plot = TRUE,
  file_name = NULL
)

Arguments

gsea_study: Output from compute_factor_gsea() on study cohort.
cancer_type: Character. TCGA cancer type abbreviation (e.g., "blca", "brca", "cesc", "chol", "coad", "skcm") identifying which pre-built TCGA meta-program file to load from inst/extdata/.
mp_file: Optional character. Path to a custom meta-program RData file. If NULL, the pre-built file for cancer_type is loaded from inst/extdata/.
plot: Logical. If TRUE (default), saves a heatmap of factor-to-meta-program scores.
file_name: Optional character. File path prefix for saving output plots.

Value

Data frame with one row per study factor: factor, best_MP, best_score, all_scores, active_hallmarks