methimputeBinomialHMM {methimpute} | R Documentation

## methimputeBinomialHMM

### Description

The `methimputeBinomialHMM` is a list() which contains various entries (see Value section). The main entry of this object is `$data`, which contains the methylation status calls and posterior values. See Details for a description of all columns.

### Details

The `$data` entry in this object contains the following columns:

- context The sequence context of the cytosine.

- counts Counts for methylated and total number of reads at each position.

- distance The distance in base-pairs from the previous to the current cytosine.

- transitionContext Transition context in the form "previous-current".

- posteriorMax Maximum posterior value of the methylation status call, can be interpreted as the confidence in the call.

- posteriorMeth Posterior value of the "methylated" component.

- posteriorUnmeth Posterior value of the "unmethylated" component.

- status Methylation status.

- rc.meth.lvl Recalibrated methylation level, calculated as `r$data$rc.meth.lvl = r$data$params$emissionParams$Unmethylated[data$context,] * r$data$posteriorUnmeth + r$params$emissionParams$Methylated[data$context,] * r$data$posteriorMeth`, where `r` is the `methimputeBinomialHMM` object.

### Value

A list() with the following entries:

`convergenceInfo` | A list() with information about the convergence of the model fitting procedure.
`params` | A list() with fitted and non-fitted model parameters.
`params.initial` | A list() with initial values for the model parameters.
`data` | A `GRanges-class` with cytosine positions and methylation status calls.
`segments` | The `data` entry where coordinates of consecutive cytosines with the same methylation status have been merged.

### See Also

`methimpute-objects`

[Package methimpute version 1.9.0 Index]