listOntologies: Get Ontologies Available in GREAT

In cemordaunt/comethyl: An R Package for Weighted Region Comethylation Network Analysis

Get Ontologies Available in GREAT

Description

listOntologies() obtains a character vector of the available ontologies for functional enrichment analysis by GREAT for a specified version and genome build.

Usage

listOntologies(
  genome = c("hg38", "hg19", "hg18", "mm10", "mm9", "danRer7"),
  version = c("4.0.4", "3.0.0", "2.0.2"),
  verbose = TRUE
)

Arguments

genome	A character(1) giving the genome build. Supported genomes include hg38, hg19, hg18, mm10, mm9, and danRer7. See Details.
version	A character(1) specifying the version of GREAT. Possible values include 4.0.4, 3.0.0, and 2.0.2. Different versions of GREAT support different genomes. See Details.
verbose	A logical(1) indicating whether messages should be printed.

Details

listOntologies() generates the possible ontologies to use for functional enrichment analysis in enrichModule(). Supported ontologies may change over time, so this function queries GREAT using the rGREAT package to get the ones currently available.

GREAT supports different genomes depending on the version:

GREAT v4.0.4

hg38, hg19, mm10, mm9

GREAT v3.0.0

hg19, mm10, mm9, danRer7

GREAT v2.0.2

hg19, hg18, mm9, danRer7

Value

A character vector.

See Also

• getModules() to build a comethylation network and identify modules of comethylated regions.

• annotateModule() and getGeneList() to annotate a set of regions with genes and regulatory context and then extract the gene symbols or IDs.

• enrichModule() and plotEnrichment() to investigate functional enrichment of module regions with GREAT.

Examples

## Not run: 

# Get Comethylation Modules
modules <- getModules(methAdj, power = sft$powerEstimate, regions = regions,
                      corType = "pearson", file = "Modules.rds")

# Annotate Modules
regionsAnno <- annotateModule(regions, module = "bisque4",
                              genome = "hg38",
                              file = "Annotated_bisque4_Module_Regions.txt")
geneList_bisque4 <- getGeneList(regionsAnno, module = "bisque4")

# Analyze Functional Enrichment
ontologies <- listOntologies("hg38", version = "4.0.4")
enrich_bisque4 <- enrichModule(regions, module = "bisque4",
                               genome = "hg38",
                               file = "bisque4_Module_Enrichment.txt")
plotEnrichment(enrich_bisque4,
               file = "bisque4_Module_Enrichment_Plot.pdf")

## End(Not run)

cemordaunt/comethyl documentation built on Oct. 20, 2023, 5:47 p.m.