plotUniprotKBFeatures {maser} | R Documentation |
Mapping and visualization of UniprotKB protein features affected by splicing.
plotUniprotKBFeatures(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), event_id, gtf, features, zoom = FALSE, show_transcripts = FALSE, show_PSI = TRUE, ncores = 1)
events |
a maser object. |
type |
character indicating splice type. Possible values are
|
event_id |
numeric, event identifier. |
gtf |
a |
features |
a character vector indicating valid UniprotKB features. |
zoom |
logical, zoom to the genomic coordinates of the splice event. |
show_transcripts |
logical, display transcripts track. |
show_PSI |
logical, display the PSI track. |
ncores |
number of cores for multithreading (available only in OSX and Linux
machines). If Windows, |
This is a wrapper function for performing both mapping and
visualization of protein features affected by the splice event. This function
calls mapProteinFeaturesToEvents
for mapping of protein
features to splicing events.
The GViz
package is used for creating
annotation tracks for genomic visualization.
Multiple protein annotation tracks can be created using the features
argument.
a Gviz object.
## Create the maser object path <- system.file("extdata", file.path("MATS_output"), package = "maser") hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h")) hypoxia_filt <- filterByCoverage(hypoxia, avg_reads = 5) ## Ensembl GTF annotation for SRSF6 gtf_path <- system.file("extdata", file.path("GTF", "SRSF6_Ensembl85.gtf"), package = "maser") ens_gtf <- rtracklayer::import.gff(gtf_path) ## Retrieve gene specific splicing events srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6") ## Map splicing events to transcripts srsf6_mapped <- mapTranscriptsToEvents(srsf6_events, ens_gtf) ## Plot splice event, transcripts and protein features plotUniprotKBFeatures(srsf6_mapped, "SE", event_id = 33209, gtf = ens_gtf, features = c("domain"), show_transcripts = TRUE)