runBumphunter {MEAL}R Documentation

Run bumphunter

Description

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

Usage

runBumphunter(set, model, coefficient = 2, bumphunter_cutoff = 0.1,
  num_permutations = 0, bumps_max = 30000, betas = TRUE,
  check_perms = FALSE, verbose = FALSE, resultSet = 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)

bumphunter_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 bumps p-value. (Default: 0)

bumps_max

Numeric with the maximum number of bumps used in the permutation. This parameter only applies when num_permutations is greater than 0. (Default: 30000)

betas

If set is a GenomicRatioSet, should beta values be used? (Default: TRUE)

check_perms

Logical. Should we check that there are less bumps than bumps_max? This parameter only applies when num_permutations is greater than 0. (Default: TRUE)

verbose

Logical value. Should the function be verbose? (Default: FALSE)

resultSet

Should results be encapsulated in a resultSet? (Default: TRUE)

...

Further arguments passed to bumphunter.

Details

runBumphunter is a wrapper for minfi bumphunter. This function runs all the steps required prior running bumphunter from the methylation set and the formula of the model. This implementation allows running bumphunter to other objects than GenomicRatioSet. The result can be encapsulated in a ResultSet to take adavantege of its plotting capabilities.

If the user wants to run permutations to calculate p-values, this implementation can filter the bumps to avoid doing a very high number of permutations and to reduce computation time. To do so, we can set the maximum number of bumps that we want to permute with the bumps_max parameter. runBumphunter increases bumphunter_cutoff value until the number of bumps is lower than bumps_max.

Value

data.frame or resultSet with the result of bumphunter

See Also

bumphunter


[Package MEAL version 1.12.0 Index]