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 1.14.0 Index]