plotUniprotKBFeatures: Mapping and visualization of UniprotKB protein features...
In DiogoVeiga/maser: Mapping Alternative Splicing Events to pRoteins

Description Usage Arguments Details Value See Also Examples

Mapping and visualization of UniprotKB protein features affected by splicing.

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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 `c("A3SS", "A5SS", "SE", "RI", "MXE")`.
`event_id`	numeric, event identifier.
`gtf`	a `GRanges`, Ensembl or Gencode GTF using the hg38 build of the human genome.
`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, `ncores` will be set to 1 automatically.

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.

mapProteinFeaturesToEvents

## 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)