hummingbirdPostAdjustmentInternal {hummingbird} | R Documentation

## Post Adjustment algorithm (internal)

### 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)

[Package hummingbird version 1.2.0 Index]