mangoCorrection: Perform mango bias correction

In aryeelab/diffloop: Identifying differential DNA loops from chromatin topology data

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)

aryeelab/diffloop documentation built on May 12, 2019, 3:42 a.m.