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 |