hummingbirdEMinternal {hummingbird} | R Documentation

## EM Algorithm (internal)

### Description

Expectation-Maximization Algorithm for Fitting the Hidden Markov Model. This function reads in methylated and unmethylated read count data, transforms it into logarithm bin-wise data, sets up initial values and implements the EM algorithm to estimate HMM parameters and find the best sequence of hidden states based on model fitting.

### Usage

    hummingbirdEMinternal(normM, normUM, abnormM, abnormUM, pos, binSize)

### Arguments

`normM` | A matrix containing the methylated read count data of the normal group. Each column of a matrix represents a replicate and each row represents a CpG position.
`normUM` | A matrix containing the unmethylated read count data of the normal group. Each column of a matrix represents a replicate and each row represents a CpG position.
`abnormM` | A matrix containing the methylated read count data of the abnormal group. Each column of a matrix represents a replicate and each row represents a CpG position.
`abnormUM` | A matrix containing the unmethylated read count data of the abnormal group. Each column of a matrix represents a replicate and each row represents a CpG position.
`pos` | The CpG position information.
`binSize` | The size of a bin.

### 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 hummingbirdEM.

### Value

`obs` | For each bin: The predicted direction of methylation change ("0" means a predicted normal bin; "1" means a predicted hypermethylated bin; "-1" means a predicted hypomethylated bin). The distance between the current bin and the bin ahead of it, the start and end positions of each bin.
`normAbnorm` | The average methylation rate of normal and abnormal groups.

### See Also

Users may call the `hummingbirdEM` 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)

[Package hummingbird version 1.2.0 Index]