[,loops,numeric,numeric,missing-method
                        Extract parts of a loops object
addchr                  Add 'chr' to GRanges seqnames
annotateAnchors         Add meta data column to anchors based on
                        GRanges
annotateAnchors.bed     Add meta data column to anchors based on
                        bedgraph scores
annotateAnchors.bigwig
                        Add meta data column to anchors based on
                        .bigwig
annotateLoops           Annotate loops as Enhancer-Promoter or
                        CTCF-CTCF
annotateLoops.dge       Annotate enhancer-promoter loops with
                        differential gene expression
bedToGRanges            Read a file and make a GRanges object
calcLDSizeFactors       Compute normalizing factors for each sample
callCCDs                Compute Chromatin Contact Domains (CCDs)
computeBoundaryScores   Compute boundary scores for genomic loci in
                        between anchors
diffloop                diffloop: A package for differential DNA loop
                        calling from ChIA-PET data
dim,loops-method        See dimensions of loops object
featureTest             Combined association test for all loops in a
                        defined region
filterLoops             Filter loops
filterSpanningLoops     Retain loops spanning some genomic feature
geneinfo                Human/mouse exon locations
getHumanGenes           Get protein coding gene regions
getHumanTSS             Get Human Transcription Start Sites
getMouseGenes           Get protein coding gene regions
getMouseTSS             Get Mouse Transcription Start Sites
head,loops-method       Extract first part of loops object
human.genes             Human protein coding genes
interchromosomal        Loops between chromosomes
intrachromosomal        Loops within chromosomes
keepCTCFloops           Keep CTCF loops
keepEPloops             Keep enhancer-promoter loops
loopAssoc               Generalized differential Loop Calling
loopDistancePlot        Visualize proportion of loops at distances
loopGenes               Determine genes contained within loops
loopMetrics             Types of loops
loopPlot                Visualize looping
loopWidth               Loop widths
loops-class             A class to represent ChIA-PET interaction data
                        and annotations
loops.small             chr1:36000000-36300000 loops
loopsMake               Read preprocessed ChIA-PET data from dnaloop
loopsMake.mango         Read preprocessed ChIA-PET data from mango
loopsSubset             Subset two difloop objects
mangoCorrection         Perform mango bias correction
manyLoopPlots           Plot several loop regions
mergeAnchors            Combine nearby anchors into one peak
numAnchors              Get number of anchors in each sample
numLoops                Per-sample loop quantities
padGRanges              Pad a GRanges object
pcaPlot                 Visualize sample relationships
plotTopLoops            Plot the most significant loops
quickAssoc              Perform quick differential loop calling
quickAssocVoom          Perform quick differential loop calling
removeRegion            Remove region from loops object
removeSelfLoops         Remove self loops
rmchr                   Remove 'chr' from GRanges seqnames
sampleNames,loops-method
                        Grab/Update Sample Names
slidingWindowTest       Combined association test for all loops in a
                        defined region
splitSamples            Split samples into their own loops object
subsetLoops             Subset loops
subsetRegion            Extract region from loops object
subsetRegionAB          Retain loops that have anchors in two specified
                        regions
summary,loops-method    Link the anchors and interactions back together
tail,loops-method       Extract last part of loops object
topLoops                Grab top loops
union,loops,loops-method
                        Combine two loops objects
updateLDGroups          Update groups in colData for loops object
