# Identifying differential DNA loops from chromatin topology data

## Documentation for package ‘diffloop’ version 1.6.0

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

## Help Pages

A B C D F G H I K L M N P Q R S T U misc

diffloop-package | diffloop: A package for differential DNA loop calling from ChIA-PET data

## -- A --

addchr | Add 'chr' to GRanges seqnames
addchr-method | Add 'chr' to GRanges seqnames
annotateAnchors | Add meta data column to anchors based on GRanges
annotateAnchors-method | Add meta data column to anchors based on GRanges
annotateAnchors.bed | Add meta data column to anchors based on bedgraph scores
annotateAnchors.bed-method | Add meta data column to anchors based on bedgraph scores
annotateAnchors.bigwig | Add meta data column to anchors based on .bigwig
annotateAnchors.bigwig-method | Add meta data column to anchors based on .bigwig
annotateLoops | Annotate loops as Enhancer-Promoter or CTCF-CTCF
annotateLoops-method | Annotate loops as Enhancer-Promoter or CTCF-CTCF
annotateLoops.dge | Annotate enhancer-promoter loops with differential gene expression
annotateLoops.dge-method | Annotate enhancer-promoter loops with differential gene expression

## -- B --

bedToGRanges | Read a file and make a GRanges object
bedToGRanges-method | Read a file and make a GRanges object

## -- C --

calcLDSizeFactors | Compute normalizing factors for each sample
calcLDSizeFactors-method | Compute normalizing factors for each sample
callCCDs | Compute Chromatin Contact Domains (CCDs)
callCCDs-method | Compute Chromatin Contact Domains (CCDs)
computeBoundaryScores | Compute boundary scores for genomic loci in between anchors
computeBoundaryScores-method | Compute boundary scores for genomic loci in between anchors

## -- D --

diffloop | diffloop: A package for differential DNA loop calling from ChIA-PET data
dim-method | See dimensions of loops object

## -- F --

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
filterSpanningLoops | Retain loops spanning some genomic feature
filterSpanningLoops-method | Retain loops spanning some genomic feature

## -- G --

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
getMouseGenes | Get protein coding gene regions
getMouseGenes-method | Get protein coding gene regions
getMouseTSS | Get Mouse Transcription Start Sites
getMouseTSS-method | Get Mouse Transcription Start Sites

## -- H --

head-method | Extract first part of loops object
human.genes | Human protein coding genes

## -- I --

interchromosomal | Loops between chromosomes
interchromosomal-method | Loops between chromosomes
intrachromosomal | Loops within chromosomes
intrachromosomal-method | Loops within chromosomes

## -- K --

keepCTCFloops | Keep CTCF loops
keepCTCFloops-method | Keep CTCF loops
keepEPloops | Keep enhancer-promoter loops
keepEPloops-method | Keep enhancer-promoter loops

## -- L --

loopAssoc | Generalized differential Loop Calling
loopAssoc-method | Generalized differential Loop Calling
loopDistancePlot | Visualize proportion of loops at distances
loopDistancePlot-method | Visualize proportion of loops at distances
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 from dnaloop
loopsMake-method | Read preprocessed ChIA-PET data from dnaloop
loopsMake.mango | Read preprocessed ChIA-PET data from mango
loopsMake.mango-method | Read preprocessed ChIA-PET data from mango
loopsSubset | Subset two difloop objects
loopsSubset-method | Subset two difloop objects
loopWidth | Loop widths
loopWidth-method | Loop widths

## -- M --

mangoCorrection | Perform mango bias correction
mangoCorrection-method | Perform mango bias correction
manyLoopPlots | Plot several loop regions
manyLoopPlots-method | Plot several loop regions
mergeAnchors | Combine nearby anchors into one peak
mergeAnchors-method | Combine nearby anchors into one peak

## -- N --

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

## -- P --

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

## -- Q --

quickAssoc | Perform quick differential loop calling
quickAssoc-method | Perform quick differential loop calling
quickAssocVoom | Perform quick differential loop calling
quickAssocVoom-method | Perform quick differential loop calling

## -- R --

removeRegion | Remove region from loops object
removeRegion-method | Remove region from loops object
removeSelfLoops | Remove self loops
removeSelfLoops-method | Remove self loops
rmchr | Remove 'chr' from GRanges seqnames
rmchr-method | Remove 'chr' from GRanges seqnames

## -- S --

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
subsetRegionAB | Retain loops that have anchors in two specified regions
subsetRegionAB-method | Retain loops that have anchors in two specified regions
summary-method | Link the anchors and interactions back together

## -- T --

tail-method | Extract last part of loops object
topLoops | Grab top loops
topLoops-method | Grab top loops

## -- U --

union-method | Combine two loops objects
updateLDGroups | Update groups in colData for loops object
updateLDGroups-method | Update groups in colData for loops object

## -- misc --

[-method | Extract parts of a loops object