hummingbirdPostAdjustmentInternal: Post Adjustment algorithm (internal)

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

Description

Post Adjustment algorithm for the output of the EM. This function adjusts HMM output such that each detected DMR has a minimum length and a minimum number of CpGs in each DMR.

Usage

hummingbirdPostAdjustmentInternal(em, pos, minCpGs, minLength, maxGap)

Arguments

em	The output of the hummingbirdEMinternal function, specifically the obs object.
pos	The CpG position information.
minCpGs	The minimum number of CpGs contained in a DMR.
minLength	The minimum length of a DMR.
maxGap	The maximum gap between any two CpGs.

Details

Users do not need to call this function directly. This is a low-level function used by the higher-level function in the hummingbird package, the hummingbirdPostAdjustment.

Value

DMRs

The detected regions based on the user-defined arguments (minLength, minCpGs, and maxGap). It contains the (numbered) 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.

See Also

Users may call the hummingbirdPostAdjustment function.

Examples

library(GenomicRanges)
library(SummarizedExperiment)

# Load sample dataset containing input data 
data(exampleHummingbird)

# Run the EM (internal) function
hmmbirdEMinternalOutput <- hummingbirdEMinternal(
    normM = assays(exampleSEControl)[["normM"]],
    normUM = assays(exampleSEControl)[["normUM"]],
    abnormM = assays(exampleSECase)[["abnormM"]],
    abnormUM = assays(exampleSECase)[["abnormUM"]],
    pos = pos, binSize = 40)
                    
# Run the Post Adjustment (internal) function
hmmbirdPAinternalOutput <- hummingbirdPostAdjustmentInternal(
    em = hmmbirdEMinternalOutput$obs, 
    pos = pos, minCpGs = 10, minLength = 100, maxGap = 300)

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