Epigenomic Analysis Package Built for R (epiRomics)

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Documentation for package ‘epiRomics’ version 0.99.5

• 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