Description Usage Arguments Details Value See Also
View source: R/runBlockFinder.R
Run blockFinder to a methylation dataset. This function contains all steps of blockFinder analysis, from model.matrix creation to running the analysis.
1 2  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 pvalue. (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
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