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

Description Usage Arguments Details Value See Author(s) See Also Examples

Description

Get enrichment tables from GREAT web server

Usage

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

Arguments

job

a GreatJob-class instance

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

maximum tries

download_by

Internally used.

verbose

Whether print messages.

Details

The table contains statistics for the each term in each ontology catalogue.

Please note there is no FDR column in original tables. Users should calculate by themselves by functions such as p.adjust

Value

The returned value is a list of data frames in which each one corresponds to result for a single ontology. The structure of the data frames are same as the tables available on GREAT website.

See

availableOntologies, availableCategories

Author(s)

Zuguang gu <z.gu@dkfz.de>

See Also

availableOntologies, availableCategories

Examples

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# note the `job` was generated from GREAT 3.0.0
job = readRDS(system.file("extdata", "job.rds", package = "rGREAT"))
tb = getEnrichmentTables(job)
names(tb)
head(tb[[1]])
job

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

jokergoo/rGREAT documentation built on April 29, 2020, 6:24 p.m.