runBumphunter {MEAL} | R Documentation

## Run bumphunter

### 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`

[Package MEAL version 1.22.0 Index]