runDMRcate {MEAL} | R Documentation

## Run DMRcate

### Description

Run DMRcate to a methylation dataset. This function contains all steps of DMRcate analysis, from model.matrix creation to running the analysis.

### Usage

    runDMRcate(set, model, coefficient = 2, resultSet = FALSE, ...)

### Arguments

`set` | `GenomicRatioSet`, `eSet` derived object or `SummarizedExperiment`
`model` | Model matrix or formula to get model matrix from `set`.
`coefficient` | Numeric with the column of model matrix used in the analysis. (Default: 2)
`resultSet` | Should results be encapsulated in a `resultSet`? (Default: TRUE)
`...` | Further arguments passed to `cpg.annotate` or `dmrcate`.

### Details

runDMRcate is a wrapper for `dmrcate` function. runDMRcate runs all the steps required prior running blockFinder from the methylation set and the formula of the model. This implementation allows running blockFinder to other objects than `GenomicRatioSet`. The result can be encapsulated in a `ResultSet` to take adavantege of its plotting capabilities.

### Value

data.frame or `resultSet` with the result of `bumphunter`

### See Also

`dmrcate`, `cpg.annotate`

[Package MEAL version 1.10.1 Index]