mapTranscriptsToEvents: Mapping of splice events to Ensembl transcripts.
In DiogoVeiga/maser: Mapping Alternative Splicing Events to pRoteins

Description Usage Arguments Details Value See Also Examples

Mapping of splice events to Ensembl transcripts.

1	mapTranscriptsToEvents(events, gtf, ncores = 1)

`events`	a maser object.
`gtf`	a `GRanges` object obtained from an Ensembl or Gencode GTF file using the hg38 build of the human genome.
`ncores`	number of cores for multithreading (available only in OSX and Linux machines). If Windows, `ncores` will be set to 1 automatically.

This function performs mapping of splice events in the maser object to Ensembl transcripts by overlapping exons involved in the splice event to the transcript models provided in the GTF.

Each type of splice event requires a specific mapping procedure (described below).

The mapping will also add Uniprot identifiers when the ENST transcript encodes for a protein.

Visualization of affected transcripts can be done using plotTranscripts.

Exon skipping
Inclusion transcript(s): Transcript(s) overlapping the cassette exon, as well both flanking exons (i.e upstream and downstream exons).
Skipping transcript(s): Transcript(s) overlapping both flanking exons but not the cassettte exon.

Intron retention
Retention transcript(s): Transcript(s) overlapping exactly the retained intron.
Skipping transcript(s): Transcript(s) where intron is spliced out and overlapping both flanking exons.

Mutually exclusive exons
Exon1 transcript(s): Transcript(s) overlapping the first exon and both flanking exons.
Exon2 transcript(s): Transcript(s) overlapping the second exon and both flanking exons.

Alternative 3' and 5' splice sites
Short exon transcript(s): Transcript(s) overlapping both short and downstream exons.
Long exon transcript(s): Transcript(s) overlapping both long and downstream exons.

a maser object with transcript and protein identifiers.

plotTranscripts

## 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", 
 "Ensembl85_examples.gtf.gz"), package = "maser")
ens_gtf <- rtracklayer::import.gff(gtf_path)
 
## Retrieve gene specific splice events
srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6")

## Map splicing events to transcripts
srsf6_mapped <- mapTranscriptsToEvents(srsf6_events, ens_gtf)
head(annotation(srsf6_mapped, "SE"))