greatAnnotate: greatAnnotate

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

greatAnnotate

Description

This function allows you to analyse the gene ontologies of targeting genes by cis-regulatory regions.

Usage

greatAnnotate(
  peaks,
  assembly = "hg38",
  return_annotation = FALSE,
  return_html_report = FALSE,
  pvalue = 0.01,
  test = "binomial",
  great_rule = "basalPlusExt",
  great_adv_upstream = 5,
  great_adv_downstream = 1,
  great_adv_span = 1000,
  great_adv_twoDistance = 1000,
  great_adv_oneDistance = 1000,
  request_interval = 60,
  great_version = "4.0"
)

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.
pvalue	The adjusted p-value which is applied to filter the results, by default 0.01.
test	The statistical test used in GREAT analysis, either 'binomial' (default) or 'hypergeometric'.
great_rule	Equivalent to the rGREAT input 'rule', 'basalPlusExt' (default, basal plus extension), 'twoClosest' (two nearest genes), or 'oneClosest' (single nearest gene).
great_adv_upstream	Equivalent to the rGREAT input 'adv_upstream' (upstream extension, kb). Only applicable when 'great_rule' is 'basalPlusExt', by default 5.0 (kb).
great_adv_downstream	Equivalent to the rGREAT input 'adv_downstream' (downstream extension, kb). Only applicable when 'great_rule' is 'basalPlusExt', by default 1.0 (kb).
great_adv_span	Equivalent to the rGREAT input 'adv_span' (maximal distal region). Only applicable when 'great_rule' is 'basalPlusExt', by default 1000.0 (kb).
great_adv_twoDistance	Equivalent to the rGREAT input 'adv_twoDistance' (region range to be considered). Only applicable when 'great_rule' is 'twoClosest', by default 1000.0 (kb).
great_adv_oneDistance	Equivalent to the rGREAT input 'adv_oneDistance' (region range to be considered). Only applicable when 'great_rule' is 'oneClosest', by default 1000.0 (kb).
request_interval	The minimal gap time between two requests using greatAnnotate, by default 60 (s).
great_version	Equivalent to the rGREAT input 'version', by default 4.0.

Value

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

Examples

require(rGREAT)
require(rbokeh)
K562_CEBPB_regions <- loadPeaks(id = "MM1_HSA_K562_CEBPB")
K562_CEBPB_regions_annotation <- greatAnnotate(peaks = K562_CEBPB_regions[1:500,],
                             return_annotation = TRUE, return_html_report = TRUE)

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