runRegionAnalysis: Run different DMR detection methods
In MEAL: Perform methylation analysis

Description Usage Arguments Details Value See Also Examples

Run different DMR detection methods

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

`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)

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

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

bumphunter, blockFinder, dmrcate

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