genomeAnnotate: genomeAnnotate

In benoukraflab/TFregulomeR: TFregulomeR reveals transcription factors’ context-specific features and functions

genomeAnnotate

Description

This function allows you to annotate genomic locations of cis-regulatory regions.

Usage

genomeAnnotate(
  peaks,
  assembly = "hg38",
  return_annotation = FALSE,
  return_html_report = FALSE,
  promoter_range = c(-1000, 100),
  TTS_range = c(-100, 1000),
  server = "ca",
  TFregulome_url,
  local_db_path = NULL
)

Arguments

peaks	Required. A bed-format genomic regions in data frame.
assembly	The genome assembly of the input regions, currently supporting 'hg19', 'hg38' (default), 'mm9' and 'mm10'.
return_annotation	Either TRUE of FALSE (default). If TRUE, a data.frame containing annotation results will be returned.
return_html_report	Either TRUE of FALSE (default). If TRUE, a dynamic HTML report will be saved.
promoter_range	A numeric vector to define promoter range. By default, c(-1000, 100) defines promoters as 1000bp upstream and 100bp downstream of TSS.
TTS_range	A numeric vector to define TTS range. By default, c(-100, 1000) defines promoters as 100bp upstream and 1000bp downstream of real TTS.
server	server localtion to be linked, either 'sg' or 'ca'.
TFregulome_url	TFregulomeR server is implemented in MethMotif server. If the MethMotif url is NO more "https://bioinfo-csi.nus.edu.sg/methmotif/" or "https://methmotif.org", please use a new url.
local_db_path	The complete path to the SQLite implementation of TFregulomeR database available at "https://methmotif.org/API_ZIPPED.zip"

Value

a data.frame, or an HTML report depending on the options.

Examples

require(TxDb.Hsapiens.UCSC.hg38.knownGene)
HCT116_CEBPB_regions <- loadPeaks(id = "MM1_HSA_HCT116_CEBPB", includeMotifOnly=TRUE)
HCT116_CEBPB_regions_annotation <- genomeAnnotate(peaks = HCT116_CEBPB_regions[1:10,],
                              return_annotation = TRUE, return_html_report = TRUE)

benoukraflab/TFregulomeR documentation built on July 8, 2024, 5:03 p.m.