plotTranscripts: Mapping and visualization of Ensembl transcripts affected by...
In DiogoVeiga/maser: Mapping Alternative Splicing Events to pRoteins

Description Usage Arguments Details Value See Also Examples

Mapping and visualization of Ensembl transcripts affected by splicing.

1 2	plotTranscripts(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), event_id, gtf, zoom = FALSE, show_PSI = TRUE)

`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.

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.

a Gviz object.

mapTranscriptsToEvents

## 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)