Package 'maser' reference manual

Title:	Mapping Alternative Splicing Events to pRoteins
Description:	This package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events generated by rMATS.
Authors:	Diogo F.T. Veiga [aut, cre]
Maintainer:	Diogo F.T. Veiga <[email protected]>
License:	MIT + file LICENSE
Version:	1.23.0
Built:	2024-09-15 05:05:37 UTC
Source:	https://github.com/bioc/maser

Retrieve annotation of splicing events from a maser object.

Description

Retrieve annotation of splicing events from a maser object.

Usage

## S4 method for signature 'Maser'
annotation(object, type = c("A3SS", "A5SS", "SE", "RI",
  "MXE"))
## S4 method for signature 'Maser'
annotation(object, type = c("A3SS", "A5SS", "SE", "RI",
  "MXE"))

Arguments

`object`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a data.frame.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(annotation(hypoxia, "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(annotation(hypoxia, "SE"))

Query available human protein features in UniprotKB.

Description

Query available human protein features in UniprotKB.

Usage

availableFeaturesUniprotKB()
availableFeaturesUniprotKB()

Value

a data.frame.

Examples

head(availableFeaturesUniprotKB(), 10)
head(availableFeaturesUniprotKB(), 10)

Boxplots of PSI distributions by splicing type.

Description

Boxplots of PSI distributions by splicing type.

Usage

boxplot_PSI_levels(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
boxplot_PSI_levels(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`

Value

a ggplot object.

Examples

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)
boxplot_PSI_levels(hypoxia_filt, type = "RI")
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)
boxplot_PSI_levels(hypoxia_filt, type = "RI")

Retrieve raw read counts values from a maser object.

Description

Retrieve raw read counts values from a maser object.

Usage

## S4 method for signature 'Maser'
counts(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
## S4 method for signature 'Maser'
counts(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`object`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a matrix.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(counts(hypoxia, "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(counts(hypoxia, "SE"))

Visualization of splicing events annotation using an interactive data table.

Description

Visualization of splicing events annotation using an interactive data table.

Usage

display(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
display(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`

Value

a datatables object.

Examples

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)
hypoxia_top <- topEvents(hypoxia_filt)
display(hypoxia_top, type = "SE")
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)
hypoxia_top <- topEvents(hypoxia_filt)
display(hypoxia_top, type = "SE")

Dotplot representation of splicing events.

Description

Dotplot representation of splicing events.

Usage

dotplot(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), fdr = 0.05,
  deltaPSI = 0.1)
dotplot(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), fdr = 0.05,
  deltaPSI = 0.1)

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`
`fdr`	numeric, FDR (False Discovery Rate) cutoff.
`deltaPSI`	numeric, absolute minimum PSI (Percent spliced-in) change

Value

a ggplot object.

Examples

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)
dotplot(hypoxia_filt, type = "SE")
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)
dotplot(hypoxia_filt, type = "SE")

Filter splicing events based on coverage.

Description

Filter splicing events based on coverage.

Usage

filterByCoverage(events, avg_reads = 5)
filterByCoverage(events, avg_reads = 5)

Arguments

`events`	a maser object.
`avg_reads`	numeric, average number of reads covering the splice event.

Value

a maser object.

Examples

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)
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)

Filter splicing events based on event identifier and type.

Description

Filter splicing events based on event identifier and type.

Usage

filterByEventId(events, event_id, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
filterByEventId(events, event_id, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`events`	a maser object.
`event_id`	numeric vector of event identifiers.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a maser object.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
filterByEventId(hypoxia, 33208, "SE")
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
filterByEventId(hypoxia, 33208, "SE")

Retrieve splicing events for a given gene.

Description

Retrieve splicing events for a given gene.

Usage

geneEvents(events, geneS, fdr = 0.05, deltaPSI = 0.1)
geneEvents(events, geneS, fdr = 0.05, deltaPSI = 0.1)

Arguments

`events`	a maser object.
`geneS`	a character indicating the gene symbol.
`fdr`	numeric, FDR cutoff.
`deltaPSI`	numeric, minimum PSI change.

Value

a maser object.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
hypoxia_mib2 <- geneEvents(hypoxia, "MIB2")
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
hypoxia_mib2 <- geneEvents(hypoxia, "MIB2")

Retrieve genomic ranges of splicing events from a maser object.

Description

Retrieve genomic ranges of splicing events from a maser object.

Usage

## S4 method for signature 'Maser'
granges(x, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), ...)
## S4 method for signature 'Maser'
granges(x, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), ...)

Arguments

`x`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.
`...`	additional arguments.

Value

a GRangesList.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(granges(hypoxia, type = "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(granges(hypoxia, type = "SE"))

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)
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.

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"))

## 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"))

Mapping of splice events to Ensembl transcripts.

Description

Mapping of splice events to Ensembl transcripts.

Usage

mapTranscriptsToEvents(events, gtf, ncores = 1)
mapTranscriptsToEvents(events, gtf, ncores = 1)

Arguments

`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.

Details

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.

Value

a maser object with transcript and protein identifiers.

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", 
 "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"))

## 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"))

Create a maser object by importing rMATS splicing events.

Description

Create a maser object by importing rMATS splicing events.

Usage

maser(path, cond_labels, ftype = c("ReadsOnTargetAndJunctionCounts",
  "JunctionCountOnly", "JCEC", "JC"))
maser(path, cond_labels, ftype = c("ReadsOnTargetAndJunctionCounts",
  "JunctionCountOnly", "JCEC", "JC"))

Arguments

`path`	a character specifiying the folder containing rMATS output files.
`cond_labels`	a character vector of length 2 describing labels for experimental conditions.
`ftype`	a character indicating the rMATS file type. Possible values are `c("ReadsOnTargetAndJunctionCounts", "JunctionCountOnly", "JCEC", "JC")`.

Details

This function creates a maser object by importing rMATS output. ftype indicates which rMATS files to import. ReadsOnTargetandJunction or JunctionCountOnly are used in rMATS 3.2.5 or lower. Newer versions (>4.0.1) use "JCEC" or "JC" nomenclature.

Value

A maser object.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))

S4 class to represent splicing events imported from rMATS.

Description

S4 class to represent splicing events imported from rMATS.

Prinicipal component analysis of PSI distributions.

Description

Prinicipal component analysis of PSI distributions.

Usage

pca(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
pca(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`

Value

a ggplot object.

Examples

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)
pca(hypoxia_filt, type = "RI")
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)
pca(hypoxia_filt, type = "RI")

Boxplots of Percent spliced-in levels for gene events.

Description

Boxplots of Percent spliced-in levels for gene events.

Usage

plotGenePSI(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"),
  show_replicates = TRUE)
plotGenePSI(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"),
  show_replicates = TRUE)

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`
`show_replicates`	logical, add data points for individual replicates

Value

a ggplot object.

Examples

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)
hypoxia_mib2 <- geneEvents(hypoxia_filt, geneS = "MIB2")
plotGenePSI(hypoxia_mib2, type = "SE", show_replicates = TRUE)
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)
hypoxia_mib2 <- geneEvents(hypoxia_filt, geneS = "MIB2")
plotGenePSI(hypoxia_mib2, type = "SE", show_replicates = TRUE)

Mapping and visualization of Ensembl transcripts affected by splicing.

Description

Mapping and visualization of Ensembl transcripts affected by splicing.

Usage

plotTranscripts(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), event_id,
  gtf, zoom = FALSE, show_PSI = TRUE)
plotTranscripts(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), event_id,
  gtf, zoom = FALSE, show_PSI = TRUE)

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.
`zoom`	logical, zoom to the genomic coordinates of the splice event.
`show_PSI`	logical, display the PSI track.

Details

This is a wrapper function for performing both mapping and visualization of Ensembl transcripts that are compatible with the splice event. This function calls mapTranscriptsToEvents for transcript mapping, which in turn uses findOverlaps for transcript overlapping. The GViz package is used for creating annotation tracks for genomic visualization of splicing events.

Each type of splice event requires a specific overlapping rule (described below), #' and a customized Gviz plot is created for each splicing type.

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

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

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

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

Value

a Gviz object.

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

## Plot exon skipping event
plotTranscripts(srsf6_events, type = "SE", event_id = 33209, gtf = ens_gtf)

## 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")

## Plot exon skipping event
plotTranscripts(srsf6_events, type = "SE", event_id = 33209, gtf = ens_gtf)

Mapping and visualization of UniprotKB protein features affected by splicing.

Description

Mapping and visualization of UniprotKB protein features affected by splicing.

Usage

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

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 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)

## 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)

Retrieve PSI (percent spliced in) values from a maser object.

Description

Retrieve PSI (percent spliced in) values from a maser object.

Usage

PSI(events, type)
PSI(events, type)

Arguments

`events`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a matrix.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(PSI(hypoxia, "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(PSI(hypoxia, "SE"))

Retrieve PSI (percent spliced in) values from a maser object.

Description

Retrieve PSI (percent spliced in) values from a maser object.

Usage

## S4 method for signature 'Maser,character'
PSI(events, type = c("A3SS", "A5SS", "SE", "RI",
  "MXE"))
## S4 method for signature 'Maser,character'
PSI(events, type = c("A3SS", "A5SS", "SE", "RI",
  "MXE"))

Arguments

`events`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a matrix.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(PSI(hypoxia, "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(PSI(hypoxia, "SE"))

Proportion of events by splicing type.

Description

Proportion of events by splicing type.

Usage

splicingDistribution(events, fdr = 0.05, deltaPSI = 0.1)
splicingDistribution(events, fdr = 0.05, deltaPSI = 0.1)

Arguments

`events`	a maser object.
`fdr`	numeric, FDR (False Discovery Rate) cutoff.
`deltaPSI`	numeric, absolute minimum PSI (Percent spliced-in) change

Value

a ggplot object.

Examples

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)
splicingDistribution(hypoxia_filt)
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)
splicingDistribution(hypoxia_filt)

Retrieve rMATS stats of differential splicing from a maser object.

Description

Retrieve rMATS stats of differential splicing from a maser object.

Usage

## S4 method for signature 'Maser'
summary(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))
## S4 method for signature 'Maser'
summary(object, type = c("A3SS", "A5SS", "SE", "RI", "MXE"))

Arguments

`object`	a maser object.
`type`	a character indicating the splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`.

Value

a data.frame.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(summary(hypoxia, "SE"))
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))
head(summary(hypoxia, "SE"))

Filter splicing events based on false discovery rate and PSI change.

Description

Filter splicing events based on false discovery rate and PSI change.

Usage

topEvents(events, fdr = 0.05, deltaPSI = 0.1)
topEvents(events, fdr = 0.05, deltaPSI = 0.1)

Arguments

`events`	a maser object.
`fdr`	numeric, FDR (False Discovery Rate) cutoff.
`deltaPSI`	numeric, absolute minimum PSI (Percent spliced-in) change

Value

a maser object.

Examples

path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))

## To select all events with minimum 10% change in PSI, and FDR < 0.01 
hypoxia_top <- topEvents(hypoxia, fdr = 0.01, deltaPSI = 0.1)
path <- system.file("extdata", file.path("MATS_output"), package = "maser")
hypoxia <- maser(path, c("Hypoxia 0h", "Hypoxia 24h"))

## To select all events with minimum 10% change in PSI, and FDR < 0.01 
hypoxia_top <- topEvents(hypoxia, fdr = 0.01, deltaPSI = 0.1)

Volcano plot of splicing events.

Description

Volcano plot of splicing events.

Usage

volcano(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), fdr = 0.05,
  deltaPSI = 0.1)
volcano(events, type = c("A3SS", "A5SS", "SE", "RI", "MXE"), fdr = 0.05,
  deltaPSI = 0.1)

Arguments

`events`	a maser object.
`type`	character indicating splice type. Possible values are `c("A3SS", "A5SS", "SE", "RI", "MXE")`
`fdr`	numeric, FDR (False Discovery Rate) cutoff.
`deltaPSI`	numeric, absolute minimum PSI (Percent spliced-in) change

Value

a ggplot object.

Examples

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)
volcano(hypoxia_filt, type = "SE")
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)
volcano(hypoxia_filt, type = "SE")

Package 'maser'

Help Index

Retrieve annotation of splicing events from a maser object.

Description

Usage

Arguments

Value

Examples

Query available human protein features in UniprotKB.

Description

Usage

Value

Examples

Boxplots of PSI distributions by splicing type.

Description

Usage

Arguments

Value

Examples

Retrieve raw read counts values from a maser object.

Description

Usage

Arguments

Value

Examples

Visualization of splicing events annotation using an interactive data table.

Description

Usage

Arguments

Value

Examples

Dotplot representation of splicing events.

Description

Usage

Arguments

Value

Examples

Filter splicing events based on coverage.

Description

Usage

Arguments

Value

Examples

Filter splicing events based on event identifier and type.

Description

Usage

Arguments

Value

Examples

Retrieve splicing events for a given gene.

Description

Usage

Arguments

Value

Examples

Retrieve genomic ranges of splicing events from a maser object.

Description

Usage

Arguments

Value

Examples

Mapping of splice events to UniprotKB protein features.

Description

Usage

Arguments

Details

Value

See Also

Examples

Mapping of splice events to Ensembl transcripts.

Description

Usage

Arguments

Details

Value

See Also

Examples

Create a maser object by importing rMATS splicing events.

Description

Usage