plotUniprotKBFeatures: Mapping and visualization of UniprotKB protein features...

Description Usage Arguments Details Value See Also Examples

View source: R/plotGeneEvents.R

Description

Mapping and visualization of UniprotKB protein features affected by splicing.

Usage

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plotUniprotKBFeatures(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"),
  event_id, gtf, features, zoom = FALSE, show_transcripts = FALSE,
  show_PSI = TRUE, ncores = 1)

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.

features

a character vector indicating valid UniprotKB features.

zoom

logical, zoom to the genomic coordinates of the splice event.

show_transcripts

logical, display transcripts track.

show_PSI

logical, display the PSI track.

ncores

number of cores for multithreading (available only in OSX and Linux machines). If Windows, ncores will be set to 1 automatically.

Details

This is a wrapper function for performing both mapping and visualization of protein features affected by the splice event. This function calls mapProteinFeaturesToEvents for mapping of protein features to splicing events.

The GViz package is used for creating annotation tracks for genomic visualization.

Multiple protein annotation tracks can be created using the features argument.

Value

a Gviz object.

See Also

mapProteinFeaturesToEvents

Examples

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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", 
   "SRSF6_Ensembl85.gtf"), package = "maser")
ens_gtf <- rtracklayer::import.gff(gtf_path)

## Retrieve gene specific splicing events
srsf6_events <- geneEvents(hypoxia_filt, geneS = "SRSF6")

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

## Plot splice event, transcripts and protein features
plotUniprotKBFeatures(srsf6_mapped, "SE", event_id = 33209, gtf = ens_gtf, 
  features = c("domain"), show_transcripts = TRUE)

DiogoVeiga/maser documentation built on Feb. 10, 2022, 10:10 a.m.