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Derive TME meta-programs by clustering Hallmarks across NMF factors

derive_meta_programs.Rd

Hierarchically clusters Hallmark gene sets by their NES profile across NMF factors to identify recurrent transcriptional programs in the TME. Optionally annotates each NMF factor with a Bagaev et al. (2021) MFP subtype (IE, IE/F, F, D) when Z, annot, and cancer_name are all supplied.

Usage

derive_meta_programs(gsea_results, k = NULL, file_name = NULL, plot = TRUE)

Arguments

gsea_results

A list of GSEA result data frames (one per NMF factor), as returned by compute_factor_gsea().

k

Integer. Number of meta-programs (clusters) to extract. If NULL (default), estimated automatically from the dendrogram.

file_name

Optional character. File path prefix for saving output plots.

plot

Logical. If TRUE (default), saves a clustering heatmap.

Value

A list with:

  • meta_programs: Named list mapping meta-program labels to character vectors of Hallmark names.

  • hallmark_clusters: Data frame with columns Hallmark, meta_program, and mean_NES.

  • heatmap: The pheatmap object.

  • k: The number of meta-programs used.

  • factor_mfp: (Only when Z, annot, and cancer_name are provided) Data frame with columns factor, best_MFP, cor_IE, cor_IEF, cor_F, cor_D, n_samples.