fugi: Further Utilities for Genomic Interactions

#' Example HiC dataset
#' 
#' This dataset contains HiC data from Seitan et al. (2013). 
#' The data was analysed using HOMER (Heinz et al. 2010) at a resolution of 100kb to find significant interactions. 
#' This example dataset has been filtered to retain only interactions on chromosomes 14 and 15 with a FDR < 0.1.
#' The data has also been annotated for overlaps with Refseq promoters.
#' See the HiC analysis vignette (\code{vignette(package="fugi")}) for more information on how this dataset was created.
#' 
#' @name hic_example_data
#' @docType data
#' @keywords datasets
#' @usage data(hic_example_data)
#' @format A \linkS4class{GenomicInteractions} object with length 8171.
#' 
#' @return A \linkS4class{GenomicInteractions} object.
#'
#' @references 
#' Seitan VC et al. (2013).
#' Cohesin-based chromatin interactions enable regulated gene expression within pre-existing architectural compartments. 
#' \emph{Genome Res.} 23, 2066-77.
#' 
#' Heinz S, Benner C, Spann N, Bertolino E et al. (2010).
#' Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. 
#' \emph{Mol. Cell} 38(4), 576-589.
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#' Mouse Refseq promoters from chr 14-15
#' 
#' This dataset contains a subset of the promoters from the Refseq annotation for mouse genome build mm9. 
#' See the HiC analysis vignette (\code{vignette(package="fugi")}) for more information on how this dataset was created.
#' 
#' @name mm9_refseq_promoters
#' @docType data
#' @keywords datasets
#' @usage data(mm9_refseq_promoters)
#' @format A \linkS4class{GRanges} object with length 2441.
#' @return A \linkS4class{GRanges} object.
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#' Human Refseq transcripts from chr 17-18
#' 
#' This dataset contains a subset of the transcripts from the Refseq annotation for human genome build hg19.
#' See the ChIA-PET analysis vignette (\code{vignette(package="fugi")}) for more information on how this dataset was created.
#' 
#' @name hg19.refseq.transcripts
#' @docType data
#' @keywords datasets
#' @usage data(hg19.refseq.transcripts)
#' @format A \linkS4class{GRanges} object with length 2441.
#' @return A \linkS4class{GRanges} object.
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#' Putative enhancers from mouse thymus data
#' 
#' This dataset contains a set of mouse thymus enhancers derived from ChIP-seq data from mouse thymus, 
#' as described in Shen et al. (2012). 
#' See the HiC analysis vignette (\code{vignette(package="fugi")}) for more details. 
#' 
#' @name thymus_enh
#' @docType data
#' @keywords datasets
#' @usage data("thymus_enhancers")
#' @format A \linkS4class{GRanges} object.
#' @return A \linkS4class{GRanges} object.
#' @references 
#' Shen Y et al. (2012).
#' A map of cis-regulatory sequences in the mouse genome. 
#' \emph{Nature} 488, 116-120.
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