mangoCorrection {diffloop} | R Documentation

## Perform mango bias correction

### Description

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

### Usage

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

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

### Arguments

`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

### Details

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.

### Value

A loops object where loops are filtered using mango bias correction

### Examples

    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)

[Package diffloop version 1.12.0 Index]