MACP (version 0.1.0)

enrichmentCPX: Functional Enrichment Analysis for Predicted Complexes

Description

This function uses gost function in gprofiler2 package to perform functional enrichment analysis for predicted modules.

Usage

enrichmentCPX(
  predcpx,
  threshold = 0.05,
  sources = c("GO", "KEGG", "CORUM", "REAC", "CORUM"),
  p.corrction.method = "bonferroni",
  custom_bg = NULL,
  org = "mmusculus"
)

Value

A data.frame with the enrichment analysis results.

Arguments

predcpx

A data.frame containing predicted complexes resulted from get_clusters or MCL_clustering.

threshold

Custom p-value threshold for significance.

sources

A vector of data sources to use. See gost for more details.

p.corrction.method

The algorithm used for multiple testing correction;defaults to 'bonferroni'. See gost for more details.

custom_bg

vector of gene names to use as a statistical background. Defaults to NULL.

org

An organism name;defaults to 'mmusculus'. See gost for more details.

Author

Matineh Rahmatbakhsh,

Details

enrichmentCPX