enrichment_modules: Calculate enrichment scores

In mlist/SPONGE: Sparse Partial Correlations On Gene Expression

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)

mlist/SPONGE documentation built on Feb. 12, 2023, 1:22 a.m.