rGREAT (version 1.4.2)

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

Description

Get enrichment tables from GREAT web server

Usage

## S3 method for class 'GreatJob':
getEnrichmentTables(job, ontology = NULL, category = "GO",
    request_interval = 30, max_tries = 100)

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

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

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

See Also

availableOntologies, availableCategories

Examples

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")