plotTranscripts: Mapping and visualization of Ensembl transcripts affected by...

In maser: Mapping Alternative Splicing Events to pRoteins

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)

maser documentation built on March 16, 2021, 6:01 p.m.