plotRegionGeneAssociations-GreatJob-method: Plot region-gene associations

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

Plot region-gene associations

Description

Plot region-gene associations

Usage

## S4 method for signature 'GreatJob'
plotRegionGeneAssociations(object, ontology = NULL, term_id = NULL, which_plot = 1:3,
    request_interval = 10, max_tries = 100, verbose = great_opt$verbose)

Arguments

object	A GreatJob-class object returned by submitGreatJob.
ontology	A single ontology names. Valid values are in availableOntologies.
term_id	Term id in the selected ontology
which_plot	Which plots to draw? The value should be in 1, 2, 3. See "Details" section for explanation.
request_interval	Time interval for two requests. Default is 300 seconds.
max_tries	Maximal times for automatically reconnecting GREAT web server.
verbose	Whether to show messages.

Details

There are following figures:

• Association between regions and genes (which_plot = 1).

• Distribution of distance to TSS (which_plot = 2).

• Distribution of absolute distance to TSS (which_plot = 3).

If ontology and term_id are set, only regions and genes corresponding to selected ontology term will be used. Valid value for ontology is in availableOntologies and valid value for term_id is from 'id' column in the table which is returned by getEnrichmentTables.

Author(s)

Zuguang gu <[e-mail]>

Examples

job = readRDS(system.file("extdata", "GreatJob.rds", package = "rGREAT"))

plotRegionGeneAssociations(job)
plotRegionGeneAssociations(job, which_plot = 1)
# Do not use other term_id for this example, or you need to generate a new `job` object.
plotRegionGeneAssociations(job, ontology = "GO Molecular Function",
    term_id = "GO:0004984")

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