expressionToRWFeatures: Gene expression to gene seeds to RWR on PPI into FGSEA scores

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

Gene expression to gene seeds to RWR on PPI into FGSEA scores

Description

Conveniently wraps RWRFGSEA using retrieveDiseaseGenesOT for disease associated genes, STRINGdb human PPI as a network, msigdbr for gene set annotations and biomaRt for matching gene IDs.

Usage

expressionToRWFeatures(
  dat,
  disease_id,
  otp_score = "association_score.datatypes.rna_expression",
  otp_cutoff = 0,
  ppi_cutoff = 700,
  pw_min.size = 5,
  pw_max.size = 200,
  dat_gene_key = "SYMBOL",
  gs_subcats = c("BP", "MF", "CP:KEGG", "CP:REACTOME"),
  directed_ppi = FALSE,
  ...
)

Arguments

dat	A gene expression matrix with samples on columns.
disease_id	Integer ID in Open Targets platform.
otp_score	Name of association score column in Open Targets.
otp_cutoff	Numeric association score cutoff for Open Targets platform genes.
ppi_cutoff	Numeric PPI link score cutoff.
pw_min.size	Minimum gene set size to use.
pw_max.size	Maximum gene set size to use.
dat_gene_key	Data gene annotation type.
gs_subcats	Gene set subcategories in msigdbr to retrieve for enrichment analysis.
directed_ppi	Whether to generate a directed network.
...	extra arguments are passed on to RWRFGSEA

Value

list of enrichment scores

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