mapProteinFeaturesToEvents {maser} | R Documentation

## Mapping of splice events to UniprotKB protein features.

### Description

Mapping of splice events to UniprotKB protein features.

### Usage

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

### Arguments

`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.

### Details

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`.

### Value

a maser object with protein feature annotation.

### See Also

`plotUniprotKBFeatures`

### 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 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"))

[Package maser version 1.2.0 Index]