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

## 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.