# Annotation of Genomic Regions to Genomic Annotations

## Documentation for package ‘annotatr’ version 1.2.1

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

## Help Pages

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_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.
builtin_annotations | Function listing which annotations are available.
builtin_genomes | Function returning supported TxDb.* genomes
check_annotations | Function to check for valid annotations
expand_annotations | Function to expand annotation shortcuts
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_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
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_regions | Read genomic regions in BEDX+Y format
reformat_hmm_codes | Function to recode classes from chromHMM type column
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_numerical | Summarize numerical data over groupings of annotated regions
tidy_annotations | Function to tidy up annotation accessors for visualization