runRegionAnalysis {MEAL} | R Documentation

## Run different DMR detection methods

### Description

Run different DMR detection methods

### Usage

    runRegionAnalysis(
      set,
      model,
      methods = c("blockFinder", "bumphunter", "DMRcate"),
      coefficient = 2,
      bumphunter_params = NULL,
      blockFinder_params = NULL,
      dmrcate_params = NULL,
      verbose = FALSE,
      resultSet = TRUE
    )

### Arguments

`set` | `GenomicRatioSet`, `eSet` derived object or `SummarizedExperiment`
`model` | Model matrix representing a linear model.
`methods` | Character vector with the names of the methods used to estimate the regions. Valid names are: "blockFinder", "bumphunter" and "DMRcate".
`coefficient` | Numeric with the index of the model matrix used to perform the analysis.
`bumphunter_params` | List with other parameter passed to `runBumphunter` function.
`blockFinder_params` | List with other parameter passed to `runBlockFinder` function.
`dmrcate_params` | List with other parameter passed to `runDMRcate` function.
`verbose` | Logical value. Should the function be verbose? (Default: FALSE)
`resultSet` | Should results be encapsulated in a `resultSet`? (Default: TRUE)

### Details

This function has been deprecated and will be defunct in the new version.

### Value

List or `resultSet` with the result of the DMR detection methods.

### See Also

`bumphunter`, `blockFinder`, `dmrcate`

### Examples

    if (require(minfiData)){
    set <- ratioConvert(mapToGenome(MsetEx[1:10,]))
     model <- model.matrix(~Sample_Group, data = pData(MsetEx))
     res <- runRegionAnalysis(set, model)
     res
    }

[Package MEAL version 1.22.0 Index]