hummingbirdPostAdjustment: Post Adjustment algorithm for the output of the EM

In hummingbird: Bayesian Hidden Markov Model for the detection of differentially methylated regions

Description

This function adjusts HMM output. It enables three additional requirements on DMRs: 1) the minimum length of a DMR, 2) the minimum number of CpGs in a DMR, and 3) the maximum distance (in base pairs) between any two adjacent CpGs in a DMR.

Usage

hummingbirdPostAdjustment(experimentInfoControl, experimentInfoCase, emInfo,
                            minCpGs, minLength, maxGap)

Arguments

experimentInfoControl	A SummarizedExperiment object containing the input data for the control group: The two assays: normM, normUM and the CpG position information: pos.
experimentInfoCase	A SummarizedExperiment object containing the input data for the case group: The two assays: abnormM, abnormUM and the CpG position information: pos.
emInfo	The output GenomicRanges object of the hummingbirdEM function.
minCpGs	The minimum number of CpGs contained in a DMR. Default value: 10.
minLength	The minimum length of a DMR. Default value: 500.
maxGap	The maximum gap between any two CpGs. Default value: 300.

Value

A list of two GenomicRanges objects, the DMRs and the obsPostAdj.

DMRs

Contains the detected regions based on the user-defined arguments (minLength, minCpGs, and maxGap). It contains the refined DMRs with the start genomic position, the end genomic position, length of the region, direction of predicted methylation change ("0" indicates no significant change, "1" indicates predicted hyper-methylation, and "-1" indicates predicted hypo-methylation), and the number of CpGs.

obsPostAdj

The methylation status of each CpG site.

Examples

library(GenomicRanges)
library(SummarizedExperiment)
data(exampleHummingbird)
emInfo <- hummingbirdEM(experimentInfoControl = exampleSEControl,
                        experimentInfoCase = exampleSECase, binSize = 40)
postAdjInfo <- hummingbirdPostAdjustment(
                                    experimentInfoControl = exampleSEControl,
                                    experimentInfoCase = exampleSECase,
                                    emInfo = emInfo, minCpGs = 10,
                                    minLength = 100, maxGap = 300)

hummingbird documentation built on April 18, 2021, 6 p.m.