runRDA {MEAL} | R Documentation

## Calculate RDA for a set

### Description

Perform RDA calculation for a `AnalysisRegionResults`. Feature values will be considered the matrix X and phenotypes the matrix Y. Adjusting for covariates is done using a model matrix passed in covarsmodel.

### Usage

    runRDA(
      set,
      model,
      num_vars = ncol(model),
      range,
      betas = FALSE,
      resultSet = TRUE,
      num_permutations = 10000,
      ...
    )

### Arguments

`set` | `MethylationSet`, `ExpressionSet` or `matrix`
`model` | Model matrix or formula to get model matrix from `set`.
`num_vars` | Numeric with the number of variables in the matrix for which the analysis will be performed. Compulsory if equation is not null.
`range` | `GenomicRanges` with the region used for RDA
`betas` | If `set` is a `GenomicRatioSet`, should beta values be used? (Default: TRUE)
`resultSet` | Should results be encapsulated in a `resultSet`? (Default: TRUE)
`num_permutations` | Numeric with the number of permutations run to compute the p-value. (Default: 1e4)
`...` | Further arguments passed to `rda`.

### Value

Object of class `rda` or `resultSet`

### See Also

`rda`

### Examples

    if (require(minfiData)){
    set <- ratioConvert(mapToGenome(MsetEx[1:10,]))
    model <- model.matrix(~set$age)
    rda <- runRDA(set, model)
    rda
    }

[Package MEAL version 1.20.4 Index]