Annotation of Genomic Regions to Genomic Annotations

Documentation for package ‘annotatr’ version 1.39.17

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annotatr-package	annotatr: Annotation of Genomic Regions to Functional Annotations
annotate_regions	A function to intersect user region data with annotation data
annotations	example_annotations data
annotatr	annotatr: Annotation of Genomic Regions to Functional Annotations
annotatr_cache	A global-variable to hold custom annotations loaded in an R session
build_ah_annots	A helper function to build arbitrary annotatinos from AnnotationHub
build_annotations	A function to build annotations from TxDb.* and AnnotationHub resources
build_ccre_annots	A helper function to build ENCODE cCRE annotations.
build_cpg_annots	A helper function to build CpG related annotations.
build_enhancer_annots	A helper function to build enhancer annotations for hg19 and mm10 from FANTOM5.
build_gene_annots	A helper function to build genic annotations.
build_hmm_annots	A helper function to build chromHMM annotations for hg19 from UCSC Genome Browser.
build_lncrna_annots	A helper function to build lncRNA annotations.
build_mane_txdb	Function to build a TxDb of the MANE Select transcripts
build_txdb_annotations	Build gene annotations from any TxDb or EnsDb
build_txdb_gene_annots	A helper function to build genic annotations from a TxDb or EnsDb
builtin_annotations	Function listing which annotations are available.
builtin_annotations_table	Table of builtin annotations by genome
builtin_genomes	Function returning supported TxDb.* genomes
cached-annotations	Cached annotations
check_annotations	Function to check for valid annotations
check_regions_genome	Function to check regions and annotations are from the same genome
clear_cached_annotations	Clear cached annotations and downloads
coannotation_pairs	Function to find the pairs of annotation types on each region
download_annotation_file	Function to download a file, with retries, into the cache
expand_annotations	Function to expand annotation shortcuts
get_annotation_rname	Function to get the cache resource name of a built annotation
get_bfc	Function to get the BiocFileCache for the cache
get_cache_dir	Function to get the directory of the cache
get_cache_rids	Function to get the resource IDs of cache entries
get_cellline_from_code	Function to return cell line from chromatin annotation code
get_cellline_from_shortcut	Function to return cell line from chromatin annotation shortcut
get_chrom_aliases	Function to map any chromosome alias of a genome to its UCSC-style name
get_genark_seqinfo	Function to get the Seqinfo of a GenArk genome with UCSC-style names
get_genark_url	Function to get the URL of a file in the UCSC GenArk hub for a genome
get_gene_table	Function to map gene IDs to gene symbols, Entrez IDs, and Ensembl IDs
get_mane_summary	Function to get the MANE Select summary
get_orgdb_name	Function to get correct org.* package name based on genome
get_txdb_name	Function to get correct TxDb.* package name based on genome
list_cached_annotations	List cached annotations and downloads
load_cached_annotation	Function to load a built annotation from the cache
plot_annotation	Plot the number of regions per annotation
plot_categorical	Plot a categorical data variable over another
plot_coannotations	Plot pair-wise annotations across regions
plot_numerical	Plot numerical data over regions or regions summarized over annotations
plot_numerical_coannotations	Plot numerical data occurring in pairs of annotations
randomize_regions	Randomize Regions
read_annotations	Read custom annotations
read_ccre_bed	Function to read an ENCODE cCRE registry BED file
read_regions	Read genomic regions in BEDX+Y format
reformat_hmm_codes	Function to recode classes from chromHMM type column
save_cached_annotation	Function to save a built annotation in the cache
set_genome_seqinfo	Function to give a GRanges the seqinfo of a genome
standardize_mcols	Function to give an annotation the standard mcols
strip_id_version	Function to remove the version from Ensembl IDs
subset_order_tbl	Function to subset a tbl_df or grouped_df by a column
summarize_annotations	Summarize annotation counts
summarize_categorical	Summarize categorical data over groupings of annotated regions
summarize_genes	Summarize annotated regions by gene
summarize_numerical	Summarize numerical data over groupings of annotated regions
tidy_annotations	Function to tidy up annotation accessors for visualization
ucsc_seqlevels	Function to rename sequences to UCSC-style names