runBumphunter: Run bumphunter

In MEAL: Perform methylation analysis

Description

Run bumphunter

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

This function has been deprecated and will be defunct in the new version.

Value

data.frame or resultSet with the result of bumphunter

See Also

bumphunter

MEAL documentation built on Feb. 3, 2021, 2 a.m.