# Epigenomic Analysis Package Built for R (epiRomics)

## Documentation for package ‘epiRomics’ version 1.0.0

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

## Help Pages

epiRomics-package | epiRomics: Epigenomic Analysis Package Built for R (epiRomics)
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
annotate_enhancers | Annotate putative enhancers with functional database overlaps
annotations | Access the genomic annotations slot of an epiRomicsS4 object
annotations-method | Access the genomic annotations slot of an epiRomicsS4 object
annotations-set | Replace the annotations slot of an epiRomicsS4 object
annotations<- | Replace the annotations slot of an epiRomicsS4 object
annotations<--method | Replace the annotations slot of an epiRomicsS4 object
benchmark_enhancer_predictor | Evaluate histone marks against any curated reference database
build_database | Build epiRomics database
cache_data | Download and Cache epiRomics Example Data
call_accessible_regions | Compute per-region signal z-scores from a BigWig file
chromatin_state_categories | Return chromatin state category definitions
classify_celltype_accessibility | Classify regions by cell-type-specific binary accessibility
classify_chromatin_states | Classify genomic regions by histone chromatin state with genomic context
epiRomics | epiRomics: Epigenomic Analysis Package Built for R (epiRomics)
epiRomicsS4 | An S4 class to manage epiRomics databases and downstream results
epiRomicsS4-accessors | Accessors for the epiRomicsS4 class
epiRomicsS4-class | An S4 class to manage epiRomics databases and downstream results
filter_accessible_regions | Filter putative enhancers by chromatin accessibility evidence
filter_enhancers | Filters putative enhancers called by epiRomics_enhancers by crossing against curated FANTOM data
find_enhanceosomes | Identifies putative enhanceosome regions by cross-referencing candidate enhancer regions against co-TF enrichment
find_enhancers_by_comarks | Identifies putative enhancer regions utilizing select histone mark co-occurrence
find_putative_enhancers | Identify putative enhancer regions using rule-based histone logic
genome | Access the genome assembly name
genome-method | Access the genome assembly name
genome-set | Replace the genome assembly name
genome<- | Replace the genome assembly name
genome<--method | Replace the genome assembly name
get_cache_path | Get Path to Cached epiRomics Data (No Download)
get_regions_of_interest | Define regions of interest and filter enhanceosome by overlap
has_cache | Check Whether epiRomics Example Data is Cached
make_example_bigwig | Create a temporary synthetic BigWig file for use in examples
make_example_database | Build a synthetic epiRomicsS4 database for use in examples
make_example_enhanceosome | Build a synthetic enhanceosome result for use in examples
make_example_putative_enhancers | Build a synthetic putative-enhancer result for use in examples
maxCovBwCached | BigWig coverage calculation
maxCovFilesCached | Multiple BigWig coverage calculation
meta | Access the metadata slot of an epiRomicsS4 object
meta-method | Access the metadata slot of an epiRomicsS4 object
meta-set | Replace the metadata slot of an epiRomicsS4 object
meta<- | Replace the metadata slot of an epiRomicsS4 object
meta<--method | Replace the metadata slot of an epiRomicsS4 object
organism | Access the organism annotation package name
organism-method | Access the organism annotation package name
organism-set | Replace the organism annotation package name
organism<- | Replace the organism annotation package name
organism<--method | Replace the organism annotation package name
plot_gene_tracks | Visualize any gene locus with multi-track BigWig overlay
plot_quick_view | Quick standalone gene/region visualization from BigWig files
plot_signal_histogram | Plot signal distribution histogram for accessibility threshold selection
plot_tracks | Multi-track genomic visualization (base R graphics)
plot_tracks_fast | Multi-track genomic visualization (base R graphics)
txdb | Access the TxDb package::object identifier slot
txdb-method | Access the TxDb package::object identifier slot
txdb-set | Replace the TxDb identifier slot of an epiRomicsS4 object
txdb<- | Replace the TxDb identifier slot of an epiRomicsS4 object
txdb<--method | Replace the TxDb identifier slot of an epiRomicsS4 object