enrichmentCPX: Functional Enrichment Analysis for Predicted Complexes

In MACP: Macromolecular Assemblies from Co-Elution Profile (MACP)

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"
)

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.

Details

enrichmentCPX

Value

A data.frame with the enrichment analysis results.

Author(s)

Matineh Rahmatbakhsh, [e-mail]

MACP documentation built on March 7, 2023, 7:42 p.m.