Mapping Alternative Splicing Events to pRoteins

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Documentation for package ‘maser’ version 1.23.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

annotation-method	Retrieve annotation of splicing events from a maser object.
availableFeaturesUniprotKB	Query available human protein features in UniprotKB.
boxplot_PSI_levels	Boxplots of PSI distributions by splicing type.
counts-method	Retrieve raw read counts values from a maser object.
display	Visualization of splicing events annotation using an interactive data table.
dotplot	Dotplot representation of splicing events.
filterByCoverage	Filter splicing events based on coverage.
filterByEventId	Filter splicing events based on event identifier and type.
geneEvents	Retrieve splicing events for a given gene.
granges-method	Retrieve genomic ranges of splicing events from a maser object.
mapProteinFeaturesToEvents	Mapping of splice events to UniprotKB protein features.
mapTranscriptsToEvents	Mapping of splice events to Ensembl transcripts.
maser	Create a maser object by importing rMATS splicing events.
Maser-class	S4 class to represent splicing events imported from rMATS.
pca	Prinicipal component analysis of PSI distributions.
plotGenePSI	Boxplots of Percent spliced-in levels for gene events.
plotTranscripts	Mapping and visualization of Ensembl transcripts affected by splicing.
plotUniprotKBFeatures	Mapping and visualization of UniprotKB protein features affected by splicing.
PSI	Retrieve PSI (percent spliced in) values from a maser object.
PSI-method	Retrieve PSI (percent spliced in) values from a maser object.
splicingDistribution	Proportion of events by splicing type.
summary-method	Retrieve rMATS stats of differential splicing from a maser object.
topEvents	Filter splicing events based on false discovery rate and PSI change.
volcano	Volcano plot of splicing events.