GSEAGO_Builder: GO enrichment for module names

In Rvirgenslane/GmicR: Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immune-Cell network (GMIC)

Description

GO enrichment for module names

Usage

GSEAGO_Builder(
  Auto_WGCNA_OUTPUT,
  species = "Homo sapiens",
  no_cores = 4,
  ontology = "BP",
  GO_conditional = FALSE,
  colname_correct = TRUE
)

Arguments

Auto_WGCNA_OUTPUT	output from Auto_WGCNA function.
species	either 'Homo sapiens' (default) or 'Mus musculus'.
no_cores	Number of cores to use. Default = 4.
ontology	string either 'BP'(Biological Process; default), 'CC'(Cellular Component), or 'MF' (Molecular Function).
GO_conditional	A logical indicating whether the calculation should condition on the GO structure. will not be carried out. If TRUE,
colname_correct	a logical value. If TRUE (default), "." in gene names will be replaced with "-". This corrects a name change that is induced by R when creating a data.frame. If FALSE, no changes will be made.

Value

Lists with gene ontology enrichment analysis, performed using GOstats, for each module.

Note

gene names must be official gene symbol

Examples

GMIC_Builder_dir<-system.file("extdata", "GMIC_Builder.Rdata", 
                              package = "GmicR", mustWork = TRUE)
load(GMIC_Builder_dir)
GMIC_Builder$GSEAGO_Builder_Output<-NULL
Test_GMIC_Builder<-GSEAGO_Builder(GMIC_Builder, no_cores = 1)
summary(Test_GMIC_Builder$GSEAGO_Builder_Output)

Rvirgenslane/GmicR documentation built on Feb. 5, 2020, 4:08 a.m.