getGeneList: Extract a Gene List from Annotated Regions

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

Extract a Gene List from Annotated Regions

Description

getGeneList() takes a data.frame of regions annotated with gene information and extracts a vector of unique gene symbols, descriptions, or IDs.

Usage

getGeneList(
  regions_annotated,
  module = NULL,
  type = c("symbol", "description", "ensemblID", "entrezID"),
  verbose = TRUE
)

Arguments

regions_annotated	A data.frame of regions with gene annotations, typically produced by annotateModule().
module	A character giving the name of one or more modules to include. If null, all modules will be included.
type	A character(1) specifying the type of gene information to extract. Possible values include symbol, description, ensemblID and entrezID.
verbose	A logical(1) indicating whether messages should be printed.

Details

getGeneList() is designed to be used in combination with annotateModule(). regions can be filtered for one or more modules of interest. Values that can be extracted include gene symbol, description, ensemblID and entrezID.

Value

A vector of unique values.

See Also

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

• annotateModule() to annotate a set of regions with genes and regulatory context.

• listOntologies(), 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.