Differential DNA loop calling from ChIA-PET data


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Documentation for package ‘diffloop’ version 1.0.2

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diffloop-package diffloop: A package for differential DNA loop calling from ChIA-PET data
addchr Add 'chr' to GRanges seqnames
addchr-method Add 'chr' to GRanges seqnames
annotateAnchors Add meta data column to anchors based on .bed file
annotateAnchors-method Add meta data column to anchors based on .bed file
annotateLoops Annotate loops as Enhancer-Promoter or CTCF-CTCF
annotateLoops-method Annotate loops as Enhancer-Promoter or CTCF-CTCF
bedToGRanges Read a file and make a GRanges object
bedToGRanges-method Read a file and make a GRanges object
calcLDSizeFactors Compute normalizing factors for each sample
calcLDSizeFactors-method Compute normalizing factors for each sample
diffloop diffloop: A package for differential DNA loop calling from ChIA-PET data
dim-method See dimensions of loops object
featureTest Combined association test for all loops in a defined region
featureTest-method Combined association test for all loops in a defined region
filterLoops Filter loops
filterLoops-method Filter loops
geneinfo Human/mouse exon locations
getHumanGenes Get protein coding gene regions
getHumanGenes-method Get protein coding gene regions
getHumanTSS Get Human Transcription Start Sites
getHumanTSS-method Get Human Transcription Start Sites
head-method Extract first part of loops object
human.genes Human protein coding genes
human.TSS Human 60k+ transcription start sites
interchromosomal Loops between chromosomes
interchromosomal-method Loops between chromosomes
intrachromosomal Loops within chromosomes
intrachromosomal-method Loops within chromosomes
loopFit Fit model for association testing
loopfit A class to represent ChIA-PET interaction data and an edgeR fit.
loopfit-class A class to represent ChIA-PET interaction data and an edgeR fit.
loopFit-method Fit model for association testing
loopGenes Determine genes contained within loops
loopGenes-method Determine genes contained within loops
loopMetrics Types of loops
loopMetrics-method Types of loops
loopPlot Visualize looping
loopPlot-method Visualize looping
loops A class to represent ChIA-PET interaction data and annotations
loops-class A class to represent ChIA-PET interaction data and annotations
loops.small chr1:36000000-36300000 loops
loopsMake Read preprocessed ChiA-PET data
loopsMake-method Read preprocessed ChiA-PET data
loopsSubset Subset two difloop objects
loopsSubset-method Subset two difloop objects
loopTest Differential Loop Calling
loopTest-method Differential Loop Calling
loopWidth Loop widths
loopWidth-method Loop widths
mergeAnchors Combine nearby anchors into one peak
mergeAnchors-method Combine nearby anchors into one peak
numAnchors Get number of anchors in each sample
numAnchors-method Get number of anchors in each sample
numLoops Per-sample loop quantities
numLoops-method Per-sample loop quantities
padGRanges Pad a GRanges object
padGRanges-method Pad a GRanges object
pcaPlot Visualize sample relationships
pcaPlot-method Visualize sample relationships
plotTopLoops Plot the most significant loops
plotTopLoops-method Plot the most significant loops
quickAssoc Perform quick differential loop calling
quickAssoc-method Perform quick differential loop calling
removeSelfLoops Remove self loops
removeSelfLoops-method Remove self loops
rmchr Remove 'chr' from GRanges seqnames
rmchr-method Remove 'chr' from GRanges seqnames
sampleNames-method Grab/Update Sample Names
sampleNames<--method Grab/Update Sample Names
slidingWindowTest Combined association test for all loops in a defined region
slidingWindowTest-method Combined association test for all loops in a defined region
splitSamples Split samples into their own loops object
splitSamples-method Split samples into their own loops object
subsetLoops Subset loops
subsetLoops-method Subset loops
subsetRegion Extract region from loops object
subsetRegion-method Extract region from loops object
summary-method Link the anchors and interactions back together
tail-method Extract last part of loops object
topLoops Grab top loops
topLoops-method Grab top loops
union-method Combine two loops objects
updateLDGroups Update groups in colData for loops object
updateLDGroups-method Update groups in colData for loops object
[-method Extract parts of a loops object