Learn R Programming

diffloop (version 1.0.2)

Differential DNA loop calling from ChIA-PET data

Description

A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments.

Copy Link

Version

Version

1.0.2

License

MIT + file LICENSE

Maintainer

Caleb Lareau

Last Published

February 15th, 2017

Functions in diffloop (1.0.2)

calcLDSizeFactors

Compute normalizing factors for each sample
topLoops

Grab top loops
splitSamples

Split samples into their own loops object
loopWidth

Loop widths
head,loops-method

Extract first part of loops object
loops-class

A class to represent ChIA-PET interaction data and annotations
filterLoops

Filter loops
loops.small

chr1:36000000-36300000 loops
bedToGRanges

Read a file and make a GRanges object
human.TSS

Human 60k+ transcription start sites
loopGenes

Determine genes contained within loops
loopMetrics

Types of loops
featureTest

Combined association test for all loops in a defined region
intrachromosomal

Loops within chromosomes
subsetRegion

Extract region from loops object
union,loops,loops-method

Combine two loops objects
slidingWindowTest

Combined association test for all loops in a defined region
quickAssoc

Perform quick differential loop calling
annotateAnchors

Add meta data column to anchors based on .bed file
geneinfo

Human/mouse exon locations
loopsSubset

Subset two difloop objects
loopFit

Fit model for association testing
numLoops

Per-sample loop quantities
plotTopLoops

Plot the most significant loops
mergeAnchors

Combine nearby anchors into one peak
numAnchors

Get number of anchors in each sample
annotateLoops

Annotate loops as Enhancer-Promoter or CTCF-CTCF
rmchr

Remove 'chr' from GRanges seqnames
diffloop

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

Remove self loops
loopTest

Differential Loop Calling
getHumanTSS

Get Human Transcription Start Sites
tail,loops-method

Extract last part of loops object
pcaPlot

Visualize sample relationships
addchr

Add 'chr' to GRanges seqnames
interchromosomal

Loops between chromosomes
dim,loops-method

See dimensions of loops object
loopfit-class

A class to represent ChIA-PET interaction data and an edgeR fit.
padGRanges

Pad a GRanges object
updateLDGroups

Update groups in colData for loops object
human.genes

Human protein coding genes
loopPlot

Visualize looping
summary,loops-method

Link the anchors and interactions back together
subsetLoops

Subset loops
loopsMake

Read preprocessed ChiA-PET data
sampleNames,loops-method

Grab/Update Sample Names
getHumanGenes

Get protein coding gene regions
[,loops,numeric,numeric,missing-method

Extract parts of a loops object