Description Usage Arguments Details Value See Author(s) See Also Examples
Get enrichment tables from GREAT web server
1 2 3 4 | ## S4 method for signature 'GreatJob'
getEnrichmentTables(job, ontology = NULL, category = "GO",
request_interval = 10, max_tries = 100, download_by = c("json", "tsv"),
verbose = TRUE)
|
job |
a |
ontology |
ontology names. Valid values are in |
category |
Pre-defined ontology categories. One category can contain more than one ontologies. Valid values are in |
request_interval |
time interval for two requests. Default is 300 seconds. |
max_tries |
maximum tries |
download_by |
Internally used. |
verbose |
Whether print messages. |
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
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.
availableOntologies
, availableCategories
Zuguang gu <z.gu@dkfz.de>
availableOntologies
, availableCategories
1 2 3 4 5 6 7 8 9 | # 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")
|
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