runBumphunter: Run bumphunter

Description Usage Arguments Details Value See Also

View source: R/runBumphunter.R

Description

Run bumphunter

Usage

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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.