MineICAParams {MineICA} | R Documentation

## Class to contain parameters for the analysis of an ICA decomposition.

### Description

Container for parameters used during the analysis of an ICA decomposition obtained on genomics data.

### Creating Objects

`new("MineICAParams")`

`new("MineICAParams", resPath="", genesPath="ProjByComp", pvalCutoff=0.05, selCutoff=3)`

### Slots

`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 (typically expression data) on which the decomposition was calculated.

`annotfile`

  Either a RData or txt file containing the annotation data for the samples (must be of dimensions samples*annotations).

`resPath`

  The path where the outputs of the analysis will be written.

`genesPath`

  The path _within_ the resPath where the gene projections will be written. If missing, will be automatically attributed as resPath/gene2components/.

`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 on the absolute feature/gene projection values to consider gene as contributing to a component, 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 use a specific threshold for each component.

### Methods

For any slot:

`slotName(MineICAParams)` and `slotName(MineICAParams)<-`:

  Accessing and setting any slot of name `slotName` contained in an MineICAParams object.

`MineICAParams["slotName"]` and `MineICAParams["slotName"]<-`:

  Accessing and setting any slot of name `slotName` contained in an MineICAParams object.

### Author(s)

Anne Biton

### See Also

`MineICAParams-class`, `runAn`.

### Examples

    # create an instance of LocSet
    new("MineICAParams")

[Package MineICA version 1.26.0 Index]