# Differential DNA loop calling from ChIA-PET data

## Documentation for package ‘diffloop’ version 1.0.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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