plotRegionGeneAssociationGraphs-GreatJob-method: Plot region-gene association figures

Description Usage Arguments Details Value Author(s) Examples

Description

Plot region-gene association figures

Usage

1
2
3
4
## S4 method for signature 'GreatJob'
plotRegionGeneAssociationGraphs(job, type = 1:3, ontology = NULL,
    termID = NULL, request_interval = 10, max_tries = 100, verbose = TRUE,
    plot = TRUE)

Arguments

job

a GreatJob-class instance

type

type of plots, should be in 1, 2, 3. See details section for explanation

ontology

ontology name

termID

term id which corresponds to the selected ontology

request_interval

time interval for two requests. Default is 300 seconds.

max_tries

maximum tries

verbose

whether show message

plot

whether make plots

Details

Generated figures are:

If ontology and termID 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 termID is from 'id' column in the table which is returned by getEnrichmentTables.

Value

a GRanges object. Columns in metadata are:

gene

genes that are associated with corresponding regions

distTSS

distance from the regions to TSS of the associated gene

The returned values corresponds to whole input regions or only regions in specified ontology term, depending on user's setting.

If there is no gene associated with the region, corresponding gene and distTSS columns will be NA.

Author(s)

Zuguang gu <z.gu@dkfz.de>

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
# note the `job` was generated from GREAT 3.0.0
job = readRDS(system.file("extdata", "job.rds", package = "rGREAT"))

res = plotRegionGeneAssociationGraphs(job)
res

plotRegionGeneAssociationGraphs(job, type = 1)

res = plotRegionGeneAssociationGraphs(job, ontology = "GO Molecular Function",
    termID = "GO:0004984")
res

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