R/annotatr_package_doc.R

In rcavalcante/annotatr: Annotation of Genomic Regions to Genomic Annotations

#' annotatr: Annotation of Genomic Regions to Functional Annotations
#'
#' Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting functional annotations. Such annotations include those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), CpGs (CpG islands, CpG shores, CpG shelves), the non-coding genome, and enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with the above functional annotations.
#'
#' @docType package
#' @name annotatr
#'
#' @rawNamespace import(AnnotationDbi, except='select')
#' @rawNamespace import(AnnotationHub, except='query')
#' @import dplyr
#' @import ggplot2
#' @import GenomicFeatures
#' @rawNamespace import(GenomicRanges, except=c('union','setdiff','intersect','union'))
#' @importClassesFrom GenomeInfoDb Seqinfo
#' @importFrom GenomeInfoDb seqnames seqlengths
#' @importFrom IRanges IRanges
#' @importFrom S4Vectors endoapply
#' @importFrom S4Vectors splitAsList
#' @import methods
#' @importFrom readr read_tsv
#' @importFrom reshape2 melt
#' @importFrom regioneR randomizeRegions
#' @importFrom rtracklayer import import.bed
#' @importClassesFrom S4Vectors Hits Rle
#' @importFrom stats as.formula
#' @importFrom utils combn data
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