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

data.frame or `resultSet` with the result of `blockFinder`

### See Also

`blockFinder`

[Package MEAL version 1.16.0 Index]