getEnrichmentTables-GreatJob-method: Get enrichment tables from GREAT web server

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

Get enrichment tables from GREAT web server

Description

Get enrichment tables from GREAT web server

Usage

## S4 method for signature 'GreatJob'
getEnrichmentTables(object, ontology = NULL, category = "GO",
    request_interval = 10, max_tries = 100, download_by = c("json", "tsv"),
    verbose = TRUE)

Arguments

object	A GreatJob-class object returned by submitGreatJob.
ontology	Ontology names. Valid values are in availableOntologies. ontology is prior to category argument.
category	Pre-defined ontology categories. One category can contain more than one ontologies. Valid values are in availableCategories
request_interval	Time interval for two requests. Default is 300 seconds.
max_tries	Maximal times for automatically reconnecting GREAT web server.
download_by	Internally used. The complete enrichment table is provided as json data on the website, but there is no information of gene-region association. By setting download_by = 'tsv', another URL from GREAT will be envoked which also contains detailed information of which genes are associated with each input region, but due to the size of the output, only top 500 terms will be returned. So if you do not really want the gene-region association column, take the default value of this argument. The columns that contain statistics are identical.
verbose	Whether to print messages.

Value

The structure of the data frames are same as the tables available on GREAT website.

See

availableOntologies, availableCategories

Author(s)

Zuguang gu <[e-mail]>

Examples

job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))
tbl = getEnrichmentTables(job)
names(tbl)
head(tbl[[1]])
job

tbl = getEnrichmentTables(job, ontology = "GO Molecular Function")
tbl = getEnrichmentTables(job, category = "GO")

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