R: Run blockFinder

runBlockFinder {MEAL}

R Documentation

Run blockFinder

Description

Run blockFinder to a methylation dataset. This function contains all steps of blockFinder analysis, from model.matrix creation to running the analysis.

Usage

runBlockFinder(set, model, coefficient = 2, blockfinder_cutoff = 0.1,
  num_permutations = 0, resultSet = FALSE, verbose = 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)
`blockfinder_cutoff`	Numeric with the minimum cutoff to include a probe in a block. (Default: 0.1)
`num_permutations`	Numeric with the number of permutations run to compute the blocks p-value. (Default: 0)
`resultSet`	Should results be encapsulated in a `resultSet`? (Default: TRUE)
`verbose`	Logical value. Should the function be verbose? (Default: FALSE)
`...`	Further arguments passed to `blockFinder`.

Details

runBlockFinder is a wrapper for minfi blockFinder. This function 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