runRegionAnalysis: Run different DMR detection methods

Description Usage Arguments Details Value See Also Examples

Description

Run different DMR detection methods

Usage

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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

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

MEAL documentation built on Feb. 3, 2021, 2 a.m.