getEnrichmentTables-GreatJob-method {rGREAT} | R Documentation

## Get enrichment tables from GREAT web server

### Description

Get enrichment tables from GREAT web server

### Usage

    ## 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

    # 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")

[Package rGREAT version 1.22.0 Index]