rGREAT (version 1.4.2)

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

Description

Plot region-gene association figures

Usage

## S3 method for class 'GreatJob':
plotRegionGeneAssociationGraphs(job, type = 1:3, ontology = NULL,
    termID = NULL, request_interval = 30, max_tries = 100)

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

Value

• a GRanges object. Columns in metadata are:

  [object Object],[object Object]

  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.

Details

Generated figures are:

• association between regions and genes
• distribution of distance to TSS
• distribution of absolute distance to TSS

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.

Examples

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

op = par("mfrow")
par(mfrow = c(1, 3))
res = plotRegionGeneAssociationGraphs(job)
res

par(mfrow = c(1, 1))
plotRegionGeneAssociationGraphs(job, type = 1)

par(mfrow = c(1, 3))
res = plotRegionGeneAssociationGraphs(job, ontology = "GO Molecular Function",
    termID = "GO:0004984")
res

par(mfrow = op)