Package index • epiRomics

Package overview

epiRomics epiRomics-package: epiRomics: Epigenomic Analysis Package Built for R (epiRomics)

build_database(): Build epiRomics database
epiRomicsS4-class epiRomicsS4: An S4 class to manage epiRomics databases and downstream results
make_example_database(): Build a synthetic epiRomicsS4 database for use in examples
make_example_bigwig(): Create a temporary synthetic BigWig file for use in examples
make_example_putative_enhancers(): Build a synthetic putative-enhancer result for use in examples
make_example_enhanceosome(): Build a synthetic enhanceosome result for use in examples

Public getter and setter methods for every slot of the epiRomicsS4 class. Prefer these over obj@slot or methods::slot(obj, "slot").

epiRomicsS4-accessors: Accessors for the epiRomicsS4 class
annotations(): Access the genomic annotations slot of an epiRomicsS4 object
`annotations<-`(): Replace the annotations slot of an epiRomicsS4 object
meta(): Access the metadata slot of an epiRomicsS4 object
`meta<-`(): Replace the metadata slot of an epiRomicsS4 object
txdb(): Access the TxDb package::object identifier slot
`txdb<-`(): Replace the TxDb identifier slot of an epiRomicsS4 object
organism(<epiRomicsS4>): Access the organism annotation package name
`organism<-`(<epiRomicsS4>): Replace the organism annotation package name
genome(<epiRomicsS4>): Access the genome assembly name
`genome<-`(<epiRomicsS4>): Replace the genome assembly name

find_putative_enhancers(): Identify putative enhancer regions using rule-based histone logic
find_enhancers_by_comarks(): Identifies putative enhancer regions utilizing select histone mark co-occurrence
find_enhanceosomes(): Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichment
filter_enhancers(): Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data
filter_accessible_regions(): Filter putative enhancers by chromatin accessibility evidence
benchmark_enhancer_predictor(): Evaluate histone marks against any curated reference database

classify_chromatin_states(): Classify genomic regions by histone chromatin state with genomic context
chromatin_state_categories(): Return chromatin state category definitions
classify_celltype_accessibility(): Classify regions by cell-type-specific binary accessibility
call_accessible_regions(): Compute per-region signal z-scores from a BigWig file
annotate_enhancers(): Annotate putative enhancers with functional database overlaps

analyze_tf_cobinding(): Analyze statistical significance of TF co-binding at enhanceosome regions
analyze_tf_overlap(): Analyze pairwise and multi-way overlap between transcription factor binding sites
get_regions_of_interest(): Define regions of interest and filter enhanceosome by overlap

plot_quick_view(): Quick standalone gene/region visualization from BigWig files
plot_tracks() plot_tracks_fast(): Multi-track genomic visualization (base R graphics)
plot_gene_tracks(): Visualize any gene locus with multi-track BigWig overlay
plot_signal_histogram(): Plot signal distribution histogram for accessibility threshold selection

epiRomics_build_dB() epiRomics_cache_data() epiRomics_cache_path() epiRomics_has_cache() epiRomics_chromatin_states() epiRomics_chromatin_states_categories() epiRomics_enhanceosome() epiRomics_enhancer_predictor_to_ref() epiRomics_enhancers_co_marks() epiRomics_enhancers_filter() epiRomics_filter_accessible() epiRomics_annotate_putative() epiRomics_putative_enhancers() epiRomics_quick_view() epiRomics_regions_of_interest() epiRomics_tf_cobinding() epiRomics_tf_overlap() epiRomics_track_layer() epiRomics_track_layer_fast() epiRomics_track_layer_gene(): Renamed epiRomics functions