enrichment_modules: Calculate enrichment scores

View source: R/fn_spongeffects_utility.R

enrichment_modulesR Documentation

Calculate enrichment scores

Description

Calculate enrichment scores

Usage

enrichment_modules(
  Expr.matrix,
  modules,
  bin.size = 100,
  min.size = 10,
  max.size = 200,
  min.expr = 10,
  method = "OE",
  cores = 1
)

Arguments

Expr.matrix

ceRNA expression matrix

modules

Result of define_modules()

bin.size

bin size (default: 100)

min.size

minimum module size (default: 10)

max.size

maximum module size (default: 200)

min.expr

minimum expression (default: 10)

method

Enrichment to be used (Overall Enrichment: OE or Gene Set Variation Analysis: GSVA) (default: OE)

cores

number of cores to be used to calculate entichment scores with gsva or ssgsea methods. Default 1

Value

matrix containing module enrichment scores (module x samples)


biomedbigdata/SPONGE documentation built on Feb. 6, 2023, 10:19 p.m.