Mapping of splice events to Ensembl transcripts.
mapTranscriptsToEvents(events, gtf, ncores = 1)
a maser object.
number of cores for multithreading (available only in OSX and Linux
machines). If Windows,
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
Transcript(s) overlapping the cassette exon, as well both flanking exons (i.e upstream and downstream exons).
Transcript(s) overlapping both flanking exons but not the cassettte exon.
Transcript(s) overlapping exactly the retained intron.
Transcript(s) where intron is spliced out and overlapping both flanking exons.
Transcript(s) overlapping the first exon and both flanking exons.
Transcript(s) overlapping the second exon and both flanking exons.
Transcript(s) overlapping both short and downstream exons.
Transcript(s) overlapping both long and downstream exons.
a maser object with transcript and protein identifiers.
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## 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"))
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