Annotate Module Regions

annotateModule() takes a data.frame of regions with module assignments, annotates them with genes using GREAT, adds additional gene information with Ensembl BioMart, provides gene regulatory context with annotatr, and then saves this as a .txt file. Support is provided for several genomes, including hg38, hg19, hg18, mm10, mm9, and danRer7.

Usage

annotateModule(
  regions,
  module = NULL,
  grey = FALSE,
  genome = c("hg38", "hg19", "hg18", "mm10", "mm9", "danRer7"),
  includeCuratedRegDoms = FALSE,
  rule = c("basalPlusExt", "twoClosest", "oneClosest"),
  adv_upstream = 5,
  adv_downstream = 1,
  adv_span = 1000,
  adv_twoDistance = 1000,
  adv_oneDistance = 1000,
  version = c("4.0.4", "3.0.0", "2.0.2"),
  save = TRUE,
  file = "Annotated_Module_Regions.txt",
  verbose = TRUE
)

Arguments

regions

A data.frame of regions with module assignments, typically obtained from getModules().

module

A character giving the name of one or more modules to annotate. If null, all modules will be annotated.

grey

A logical(1) specifying whether or not to include the grey (unassigned) module.

genome

A character(1) giving the genome build for the regions. Supported genomes include hg38, hg19, hg18, mm10, mm9, and danRer7. See Details.

includeCuratedRegDoms

A logical(1) indicating whether to include curated regulatory domains for GREAT gene annotation.

rule

A character(1) specifying the rule used by GREAT for gene annotation. Possible values include basalPlusExt, twoClosest, and oneClosest. See rGREAT::submitGreatJob() for more details for this and the next six arguments.

adv_upstream

A numeric(1) giving the distance upstream of the TSS (in kb) to define a basal regulatory domain in the basalPlusExt rule.

adv_downstream

A numeric(1) giving the distance downstream of the TSS (in kb) to define a basal regulatory domain in the basalPlusExt rule.

adv_span

A numeric(1) specifying the distance upstream and downstream of the TSS (in kb) to define the maximum extension of the regulatory domain in the basalPlusExt rule.

adv_twoDistance

A numeric(1) giving the distance upstream and downstream of the TSS (in kb) to define the maximum extension of the regulatory domain in the twoClosest rule.

adv_oneDistance

A numeric(1) giving the distance upstream and downstream of the TSS (in kb) to define the maximum extension of the regulatory domain in the oneClosest rule.

version

A character(1) specifying the version of GREAT to use for gene annotation. Possible values include 4.0.4, 3.0.0, and 2.0.2. Different versions of GREAT support different genomes. See Details.

save

A logical(1) indicating whether to save the data.frame.

file

A character(1) giving the file name (.txt) for the saved data.frame.

verbose

A logical(1) indicating whether messages should be printed.

Value

A data.frame adding gene and regulatory annotations to the regions.

Details

regions can be filtered for one or more modules of interest, or the grey (unassigned) module can be excluded. Gene annotation is performed by the rGREAT package, which allows for different annotation rules and versions of GREAT. The default basalPlusExt annotation rule associates a gene with a region if the region is within the basal regulatory domain of the gene (5 kb upstream and 1 kb downstream of the TSS) or if it is within 1 Mb upstream or downstream of the TSS and not in the basal regulatory domain of another gene. Other rules include twoClosest and oneClosest, which effectively assign the two nearest genes or one nearest genes, respectively. See rGREAT::submitGreatJob() for more details.

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

Gene information is provided by the biomaRt package, which adds the gene description along with Ensembl and NCBI Entrez gene IDs. Regulatory context is added by the annotatr package. This provides positional context of the region relative to nearby genes, enhancers, and CpG islands. Note that annotatr does not support the hg18 or danRer7 genomes.

See also

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

• getGeneList() to extract a list of genes or IDs from the annotated regions.

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

Examples

if (FALSE) {

# 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")
}