nullrangesOldData: Datasets for the nullranges package

#' ENCODE Unified GRCh38 Exclusion List 
#'
#' The Exclusion List is a unification of three separate lists
#' followed by extensive manual curation generated by Anshul Kundaje,
#' Stanford https://www.encodeproject.org/files/ENCFF356LFX/
#'
#' Analysis script is in 'inst/script/exclude.R'.
#' 
#' @format a GRanges object
#' 
#' @docType data
#' 
#' @usage data("exclude")
#' @import GenomicRanges
"exclude"

#' DNase hypersensitivity (DHS) peaks in A549 cell example data
#'
#' An example dataset containing narrowPeak file from ENCODE. Retrieve
#' record with \code{object[["AH22505"]]} on Annotation Hub. Analysis
#' script is in 'inst/script/DHSA549Hg38.R'.
#' 
#' @format a GRanges object with metadata score, signal value,
#' p/q value and peak.
#' 
#' @docType data
#' 
#' @usage data("DHSA549Hg38")
#' 
"DHSA549Hg38"

#' Predicted CTCF-motif binding sites
#'
#' Genomic coordinates of predicted CTCF binding sites with motif
#' MA0139.1 (Jaspar), in BED format, with strand orientation
#' (directionality of binding). Human (hg19, hg38) and mouse (mm9,
#' mm10) genomes. The binding sites were detected using the FIMO tool
#' of the MEME suite using default settings. Extra columns include
#' motif name (MA0139.1), score, p-value, q-value, and the motif
#' sequence.
#' 
#' @format a GRanges object
#' 
#' @docType data
#' 
#' @usage data("CTCF_hg19")
#' 
#' @references 
#' Dozmorov MG (2021). _CTCF_. https://github.com/mdozmorov/CTCF/CTCF - R
#' package version 0.99.0, <URL: https://github.com/mdozmorov/CTCF>.
#' 
"CTCF_hg19"

#' 10Kb bins from hg19 with GM12878 metadata annotation features
#'
#' 10Kb bins were tiled across hg19 and annotated with CTCF and DNase
#' site features from GM12878. Feature annotations for each bin
#' include 1) the number of CTCF sites, 2) the CTCF signal strength
#' (from peak calls), 3) the number of DNase sites, 4) the DNase
#' signal strength (from signal tracks), and finally 5) the
#' presence/absence of a loop to any other bin.
#' 
#' @format a GRanges object with covariate metadata
#' 
#' @docType data
#' 
#' @usage data("hg19_10kb_bins")
#' 
#' 
"hg19_10kb_bins"

#' CTCF-bound 10Kb paired genomic interactions
#'
#' 10Kb bins were tiled across hg19 then subset by those which
#' contained CTCF sites. All pairs of CTCF-bound 10Kb bins were
#' generated and annotated with feature overlaps from GM12878. Feature
#' annotations include 1) presence/absence of a loop between
#' bin-pairs, 2) the total CTCF signal from both bin-pairs, 3) the
#' number of CTCF sites from both bin-pairs, 4) the distance between
#' bin-pairs, and finally 4) whether a convergent set of CTCF sites
#' exists between bin-pairs.
#' 
#' @format a GInteractions object with covariate metadata
#' 
#' @docType data
#' 
#' @usage data("hg19_10kb_ctcfBoundBinPairs")
#' @import InteractionSet
#' 
"hg19_10kb_ctcfBoundBinPairs"