buildMineICAParams {MineICA} | R Documentation

## Creates an object of class MineICAParams

### Description

This function builds an object of class `MineICAParams`. It contains the parameters that will be used by function `runAn` to analyze the ICA decomposition contained in an object of class `IcaSet`.

### Usage

      buildMineICAParams(Sfile = new("character"),
        Afile = new("character"), datfile = new("character"),
        annotfile = new("character"), resPath = "", genesPath,
        annot2col = new("character"), pvalCutoff = 0.05,
        selCutoff = 3)

### Arguments

`Sfile` | A txt file containing the Source matrix S.
`Afile` | A txt file containing the Mixing matrix A.
`datfile` | A txt file containing the data (e.g expression data) on which the decomposition was calculated.
`annotfile` | Either a "rda" or "txt" file containing the annotation data for the samples (must be of dimensions samples x annotations).
`resPath` | The path where the outputs of the analysis will be written, default is the current directory.
`genesPath` | The path _within_ the resPath where the gene projections will be written. If missing, will be automatically attributed as `resPath`/ProjByComp/.
`annot2col` | A vector of colors indexed by annotation levels. If missing, will be automatically attributed using function `annot2Color`.
`pvalCutoff` | The cutoff used to consider a p-value significant, default is 0.05.
`selCutoff` | The cutoff applied to the absolute feature/gene projection values to consider them as contributors, default is 3. Must be either of length 1 and the same treshold is applied to all components, or of length equal to the number of components in order to a specific threshold is for each component.

### Value

An object of class `MineICAParams`

### Author(s)

Anne Biton

### See Also

`MineICAParams`, `runAn`

### Examples

    ## define default parameters and fill resPath
    params <- buildMineICAParams(resPath="resMineICACarbayo/")

    ## change the default cutoff for selection of contribugint genes/features
    params <- buildMineICAParams(resPath="resMineICACarbayo/", selCutoff=4)

[Package MineICA version 1.26.0 Index]