Function reference • hictoolsr

About hictoolsr
`hictoolsr` `hictoolsr-package`	hictoolsr: a set of tools for Hi-C data analysis
Extracting Hi-C Counts
`extractCounts()`	Extract counts from .hic file(s)
`calcApa()`	Extract BEDPE interactions from a Hi-C matrix
Generating Paired Interactions
`calcBedpe()`	Calculates all potential paired interactions from a BED file
`calcPairs()`	Define function to calculate all paired interactions within a windowSize
Merging/Filtering/Binning Tools for merging, filtering, or binning paired interactions.
`binBedpe()`	Define function to flexibly bin bedpe data by hic resolution
`filterBedpe()`	Filters out short BEDPE interactions
`mergeBedpe()`	Read-in and merge BEDPE Interactions by Genomic distance with DBSCAN
`makeGInteractionsFromDataFrame()` `as_ginteractions()`	Convert DataFrames to GInteraction objects
`binAnchor()`	Define helper function for binning an anchor
`check_binned()`	Helper function to check that a GInteractions object has been binned
`shiftAnchor()`	Define helper function for flexibly shifting an anchor
Plotting Functions
`plotApa()`	Plots Aggregate Peak Analysis Matrix
Example Datasets
`loopApaFsHic`	Aggregate peak analysis of differential loop results from FS Hi-C
`loopApaWtHic`	Aggregate peak analysis of differential loop results from WT Hi-C
`loopCounts`	Merged loop calls with contact frequency from replicate Hi-C experiments

Reference