hictoolsr: Hi-C analysis in R

hictoolsr is an R package with a collection of useful tools for Hi-C data analysis. The tools in this package are optimized to quickly extract and apply data from .hic files without the use of external tools.

Future updates

Improve function naming:

• binBedpe() args a1Pos and a2Pos
• binBedpe() to mapBedpeToBin(), mapBedpeToBin(), assignBedpeToBin(), convertBedpeToBin()?
• More general names (i.e. binAnchor() -> binGRanges())?

binBedpe()

• Improve documentation and examples

calcApa()

• Improve documentation and examples

calcBepde()

• Improve documentation and examples
• Change output from data.table to GInteractions object.
• Replace internal binning method with other binning functions

extractCounts()

• Improve documentation and examples
• Change name to extractHicCounts()
• Remove excess comments in function
• Move binning warning to its own function
• Utilize the chromosome extraction method from calcApa()
  • This might remove the chromosomes argument as well.

filterBedpe()

• Improve documentation and examples
• Currently does not filter out regions that are too close to the starts and ends of chromosomes. This is not a problem (it doesn't affect how straw imports the data), but it might be desirable to have those interactions filtered out.
  • Specifically, remove starts - res*buffer and end + res*buffer in filtering.
  • Will require GRanges to have seqinfo
• Move binning warning to its own function
• Currently removes mcols after filtering - make sure to add those back in.

mergeBedpe()

• Improve documentation and examples.
• Change input to handle R objects (data.tables/GInteraction objects).
• Replace internal binning method with other binning functions.
• Change output from data.table to GInteractions object (or make this an argument).

plotApa()