runRegionAnalysis: Run different DMR detection methods

In isglobal-brge/MEAL: Perform methylation analysis and facilitates differential expression analyses

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
}

isglobal-brge/MEAL documentation built on May 8, 2021, 8:05 p.m.