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

## Documentation for package ‘SpliceImpactR’ version 1.0.0

- 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