Description Usage Arguments Details Value Author(s) Examples
Plot region-gene association figures
1 2 3 4 |
job |
a |
type |
type of plots, should be in |
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 |
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
.
a GRanges
object. Columns in metadata are:
genes that are associated with corresponding regions
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
.
Zuguang gu <z.gu@dkfz.de>
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
|
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