mangoCorrection: Perform mango bias correction
In diffloop: Identifying differential DNA loops from chromatin topology data

Description Usage Arguments Details Value Examples

mangoCorrection takes a loops object and filters loops based on the binomial model used in the mango ChIA-PET pipeline.

mangoCorrection(lo, FDR = 1, PValue = 1, nbins = 10)

## S4 method for signature 'ANY'
mangoCorrection(lo, FDR = 1, PValue = 1, nbins = 10)

`lo`	A loops object.
`FDR`	Minimum FDR value for loop to be included; default 1
`PValue`	Minimum p0value for loop to be included; default 1
`nbins`	Number of bins for mango computation

This function processes ChIA-PET data in a loops object and filters loops that may be biased due to proximity or low PET counts as previously described by the mango pipeline. PET and anchor counts are aggregated across all samples to compute statistical significance. Consider using a larger number of bins (e.g. 30) for a larger data object when possible.

A loops object where loops are filtered using mango bias correction

rda <- paste(system.file("rda", package = "diffloop"), "loops.small.rda", sep = "/")
load(rda)
loops.small <- removeSelfLoops(loops.small)
loops.small.mango <- mangoCorrection(loops.small, PValue = 0.05)