An R package to identify functional impacts due to alternative RNA processing events

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Documentation for package ‘SpliceImpactR’ version 0.99.4

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

Help Pages

add_splice_part	Add one part to an existing SpliceImpactResult
as_dt_from_s4	Convert S4 slots back to data.table
as_splice_impact_result	Build S4 SpliceImpact container
attach_sequences	Attach transcript and protein sequences to an event or annotation table
compare_hit_index	Compare HIT index values between conditions
compare_sequences_alignment	Compare isoform nucleotide and protein sequences by pairwise alignment
compare_sequence_frame	Compare frame states after sequence alignment
compare_transcript_pairs	Compare user-selected transcript pairs
enrich_by_db	Run domain enrichment by database
enrich_by_event	Run domain enrichment by event type
enrich_domains_hypergeo	Domain-level enrichment via hypergeometric test
filter_spliceimpact_hits	Filter a SpliceImpactResult by arbitrary paired-hit columns
get_annotation	Load and cache GENCODE annotations, sequences, and hybrid exon annotations
get_background	Build a transcript-pair background with domain and length annotations
get_comprehensive_annotations	Combine multiple sources of protein feature annotations
get_differential_inclusion	Differential Inclusion Analysis from Hit Index Tables
get_di_gene_enrichment	Extract Differential-Inclusion Genes for Enrichment
get_domains	Add protein domain annotations to splicing events
get_domain_gene_for_enrichment	Extract Domain-Altering Genes for Enrichment
get_enrichment	Gene Set Enrichment for Splicing-Linked Gene Lists
get_exon_features	Map protein features to coding exons
get_gene_enrichment	Unified gene selector for enrichment foregrounds
get_hitindex	Load HIT index PSI files for one or more samples/conditions.
get_hits_core	Convenience accessor for core paired-hit columns
get_hits_domain	Convenience accessor for domain-focused paired-hit columns
get_hits_final_view	Access paired-hits as compact data.table subsets
get_hits_ppi	Convenience accessor for PPI-focused paired-hit columns
get_hits_sequence	Convenience accessor for sequence/frame-focused paired-hit columns
get_manual_features	Incorporate user-supplied protein features
get_matched_events_chunked	Match splicing events to transcript annotations in chunks
get_pairs	Pair inclusion and exclusion forms of splicing events
get_ppi_gene_enrichment	Extract Protein-Interaction-Affected Genes for Enrichment
get_ppi_interactions	Pull PPI from SpliceImpactR's data
get_ppi_switches	Annotate hits_domain with PPI changes for inclusion vs exclusion forms
get_protein_features	External function to fetch protein features from biomaRt
get_proximal_shift_from_hits	Classify splicing events as proximal or distal
get_rmats	Expand rMATS event tables into scalar exon inclusion/exclusion coordinates.
get_rmats_hit	Wrapper function to get both rmats and hit index cleanly
get_rmats_post_di	Import post-differential-inclusion rMATS results
get_splicing_impact	End-to-end SpliceImpactR wrapper with selectable output class
get_user_data	Get User-Supplied Splicing Event Data
get_user_data_post_di	Format user-supplied post-DI (post-differential-inclusion) splicing results
import_di_table	Standardize a differential inclusion (DI) result table
integrated_event_summary	Integrated summary of event classification, alignment, and domain changes
keep_sig_pairs	Filter event pairs by significance and deltaPSI thresholds
load_example_data	Load bundled example inputs for documentation
load_rmats	Load rMATS event files into standardized data.tables
overview_spicing_comparison	Overview of global splicing event distributions between conditions
plot_alignment_summary	Plot alignment score distribution and coding summary
plot_di_volcano_dt	Volcano plot for differential inclusion results
plot_enriched_domains_counts	Plot enriched domains by associated event count
plot_length_comparison	Compare inclusion vs. exclusion isoform lengths
plot_ppi_summary	Plot summary of altered PPI interactions
plot_two_transcripts_with_domains_unified	Plot two transcripts with exon structure and protein feature tracks (unified view)
probe_individual_event	Visualize PSI values for a single splicing event
SpliceImpactResult-class	SpliceImpact result container (S4)
spliceimpact_s4_guide	Detailed guide for using SpliceImpactResult
spliceimpact_s4_schema	S4 slot and key schema for SpliceImpactResult