subsample_pathway_enrichment: Cross-validation wrapped pathway enrichment

In vittoriofortino84/COPS: Clustering algorithms for Omics-driven Patient Stratification

Cross-validation wrapped pathway enrichment

Description

This function wraps the pathway enrichment based data transformations for use in a 'cross-validated' clustering pipeline. Assumes a parallel backend has been registered for foreach with registerDoParallel. Setting parallel does nothing.

Usage

subsample_pathway_enrichment(
  dat_list,
  sub_index,
  gene_id_list,
  parallel = 1,
  ...
)

Arguments

dat_list	list of data.tables corresponding gene expression matrices where the gene names have been replaced by dimension IDs (dim1, dim2, ...).
sub_index	list of data.frames corresponding to cross-validation fold indicators as produced by subsampling
gene_id_list	list of gene name vectors of the corresponding columns in dat_list
parallel	ignored and set to 1 for spawned subprocesses
...	arguments passed on to genes_to_pathways

Value

list of data.frames with extracted pathway features

vittoriofortino84/COPS documentation built on Jan. 28, 2025, 3:16 p.m.