runBlockFinder: Run blockFinder

Description Usage Arguments Details Value See Also

View source: R/runBlockFinder.R

Description

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

Usage

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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


MEAL documentation built on May 24, 2018, 6:02 p.m.