mapProteinFeaturesToEvents: Mapping of splice events to UniprotKB protein features.
In maser: Mapping Alternative Splicing Events to pRoteins

Description Usage Arguments Details Value See Also Examples

Mapping of splice events to UniprotKB protein features.

1 2	mapProteinFeaturesToEvents(events, tracks, by = c("feature", "category"), ncores = 1)

`events`	a maser object with transcript and protein identifiers.
`tracks`	a character vector indicating valid UniprotKB features or categories.
`by`	a character vector, possible values are `c("feature", "category")`.
`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 splicing events to protein features available in the UniprotKB database. Annotation tracks of protein features mapped to the hg38 build of the human genome are retrieved from the public UniprotKB FTP. The function will overlap exons involved in the splice event with the feature genomic coordinates retrieved from UniprotKB.

Annotation can be executed either by feature or category. If categories are provided, all features within the category group will be included for annotation.

Thus, batch annotation is enabled either by using by = category or by providing mutilple features in the tracks argument.

Visualization of protein features can be done using plotUniprotKBFeatures.

a maser object with protein feature annotation.

plotUniprotKBFeatures

## 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 splice events
srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6")

## Map splicing events to transcripts
srsf6_mapped <- mapTranscriptsToEvents(srsf6_events, ens_gtf)

## Annotate splice events with protein domains
srsf6_annot <- mapProteinFeaturesToEvents(srsf6_mapped, tracks = "domain")
head(annotation(srsf6_annot, "SE"))