runBlockFinder {MEAL} | R Documentation |
Run blockFinder to a methylation dataset. This function contains all steps of blockFinder analysis, from model.matrix creation to running the analysis.
runBlockFinder(set, model, coefficient = 2, blockfinder_cutoff = 0.1, num_permutations = 0, resultSet = FALSE, verbose = FALSE, ...)
set |
|
model |
Model matrix or formula to get model matrix from |
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 |
verbose |
Logical value. Should the function be verbose? (Default: FALSE) |
... |
Further arguments passed to |
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.
data.frame or resultSet
with the result of blockFinder