plotTranscripts {maser} | R Documentation

## Mapping and visualization of Ensembl transcripts affected by splicing.

### Description

Mapping and visualization of Ensembl transcripts affected by splicing.

### Usage

    plotTranscripts(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), event_id,
      gtf, zoom = FALSE, show_PSI = TRUE)

### 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.
`zoom` | logical, zoom to the genomic coordinates of the splice event.
`show_PSI` | logical, display the PSI track.

### Details

This is a wrapper function for performing both mapping and visualization of Ensembl transcripts that are compatible with the splice event. This function calls `mapTranscriptsToEvents` for transcript mapping, which in turn uses `findOverlaps` for transcript overlapping. The `GViz` package is used for creating annotation tracks for genomic visualization of splicing events.

Each type of splice event requires a specific overlapping rule (described below), #' and a customized `Gviz` plot is created for each splicing type.

Exon skipping
Inclusion track

  Transcript(s) overlapping the cassette exon, as well both flanking exons (i.e upstream and downstream exons).

Skipping track

  Transcript(s) overlapping both flanking exons but not the cassettte exon.

Intron retention
Retention track

  Transcript(s) overlapping exactly the retained intron.

Skipping track

  Transcript(s) where intron is spliced out and overlapping both flanking exons.

Mutually exclusive exons
Exon1 track

  Transcript(s) overlapping the first exon and both flanking exons.

Exon2 track

  Transcript(s) overlapping the second exon and both flanking exons.

Alternative 3' and 5' splice sites
Short exon track

  Transcript(s) overlapping both short and downstream exons.

Long exon track

  Transcript(s) overlapping both long and downstream exons.

### Value

a Gviz object.

### See Also

`mapTranscriptsToEvents`

### 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")

    ## Plot exon skipping event
    plotTranscripts(srsf6_events, type = "SE", event_id = 33209, gtf = ens_gtf)

[Package maser version 1.4.0 Index]