plotUniprotKBFeatures {maser} | R Documentation

## Mapping and visualization of UniprotKB protein features affected by splicing.

### Description

Mapping and visualization of UniprotKB protein features affected by splicing.

### Usage

    plotUniprotKBFeatures(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"),
      event_id, gtf, features, zoom = FALSE, show_transcripts = FALSE,
      show_PSI = TRUE, ncores = 1)

### Arguments

`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.

### Details

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.

### Value

a Gviz object.

### See Also

`mapProteinFeaturesToEvents`

### Examples

    ## 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)

[Package maser version 1.12.1 Index]