getRegionGeneAssociations-GreatJob-method: Get region-gene associations

In jokergoo/rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions

Get region-gene associations

Description

Get region-gene associations

Usage

## S4 method for signature 'GreatJob'
getRegionGeneAssociations(object, ontology = NULL, term_id = NULL,
    request_interval = 10, max_tries = 100, verbose = great_opt$verbose)

Arguments

object	A GreatJob-class object returned by submitGreatJob.
ontology	ontology name
term_id	Term id in the selected ontology.
request_interval	Time interval for two requests. Default is 300 seconds.
max_tries	Maximal times for automatically reconnecting GREAT web server.
verbose	Whether to show messages.

Value

A GRanges object. Please the two meta columns are in formats of CharacterList and IntegerList because a region may associate to multiple genes.

Please note, the distance is from the middle points of input regions to TSS.

Author(s)

Zuguang gu <[e-mail]>

Examples

job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))

gr = getRegionGeneAssociations(job)
gr

jokergoo/rGREAT documentation built on March 28, 2024, 5:31 a.m.