View source: R/Annotate_Modules.R
getGeneList | R Documentation |
getGeneList()
takes a data.frame
of regions annotated with gene
information and extracts a vector
of unique gene symbols, descriptions,
or IDs.
getGeneList(
regions_annotated,
module = NULL,
type = c("symbol", "description", "ensemblID", "entrezID"),
verbose = TRUE
)
regions_annotated |
A |
module |
A |
type |
A |
verbose |
A |
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
.
A vector
of unique values.
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.
## 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)
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