NAMESPACE

# Generated by roxygen2: do not edit by hand

S3method(annotate,ontology)
S3method(collapse_redundant_terms,ontology)
S3method(collapse_terms,ontology)
S3method(compute_redundancy,ontology)
S3method(filter,ontology)
S3method(filter_obsolete,ontology)
S3method(filter_unannotated,ontology)
S3method(permute,ontology)
S3method(propagate_annotations,ontology)
S3method(recompute_ancestors,ontology)
S3method(unite_roots,ontology)
export(annotate)
export(collapse_redundant_terms)
export(collapse_terms)
export(compute_gene_pcs)
export(compute_redundancy)
export(compute_term_pcs)
export(compute_term_pcs_stepdown)
export(extract_pcs)
export(filter)
export(filter_obsolete)
export(filter_unannotated)
export(permute)
export(plot_hierarchy)
export(propagate_annotations)
export(read_bed)
export(read_gaf)
export(read_obo)
export(recompute_ancestors)
export(test_genes)
export(test_terms)
export(unite_roots)
importFrom(BEDMatrix,BEDMatrix)
importFrom(GenomicRanges,findOverlaps)
importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(Matrix,crossprod)
importFrom(broom,tidy)
importFrom(circlize,colorRamp2)
importFrom(corpcor,fast.svd)
importFrom(dplyr,arrange)
importFrom(dplyr,bind_rows)
importFrom(fastmatch,"%fin%")
importFrom(fastmatch,fmatch)
importFrom(future.apply,future_lapply)
importFrom(ggplot2,aes)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggplot_build)
importFrom(ggplot2,ggplot_gtable)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_gradient)
importFrom(igraph,as_ids)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,keeping_degseq)
importFrom(igraph,rewire)
importFrom(igraph,topo_sort)
importFrom(ontologyIndex,get_ancestors)
importFrom(ontologyIndex,get_descendants)
importFrom(ontologyIndex,get_ontology)
importFrom(stringr,str_to_title)
importFrom(stringr,str_wrap)