PostChicago - visualization and integration of Capture-(Hi)C data

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Documentation for package ‘PostChicago’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation

Help Pages

aggregatePeaks	Aggregate Interactions to Interaction Peaks
aggregatePeaks_regions	Aggregate Interactions to Interaction Peaks by Distance in bp
annotateInts	Annotate Interactions
baitmap2baited_genes	Convert baitmap to baited_genes
boxplotsCapC	Boxplots of summarized interactions data.
getMatrix	Create Interaction Matrices
loadCdList	Loads List with Interaction Tables
loadGrl	Load Intervals into a GenomicRangesList
makeBedGraphs	Create Bedgraphs From ChicagoData
makeIntsTable	Create Interactions Table
makeOneGeneOnePeak	Make one-Gene-one-Peak Interaction Tables.
makeQCplots	Quality Control Plots
plotAggregatePeaks	Plot Aggregate Interaction Profiles
plotInteractions	Plot Lineplots of Interactions
plotSigIntsStats	Plot Interaction Statistics
quantifyWithinPeaks	Quantification of Reads and Scores within oneGeneOnePeak or AggregatedPeak Interactions.
rmap2rmapgr	Convert .rmap to the GenomicRanges object 'rmapgr'
runChicagoForPostChicago	Run Chicago and save ChicagoData objects.