selectWitnessGenes {MineICA} | R Documentation

## selectWitnessGenes

### Description

This function selects a gene per component.

### Usage

      selectWitnessGenes(icaSet, params,
        level = c("genes", "features"), maxNbOcc = 1,
        selectionByComp = NULL)

### Arguments

`icaSet` | An object of class `IcaSet`
`params` | An object of class `MineICAParams` containing the parameters of the analysis, the attribute `cutoffSel` is used as the threshold.
`level` | The attribute of `icaSet` to be used, the witness elements will be either selected within the `"features"` or the `"genes"`
`maxNbOcc` | The maximum number of components where the genes can have an absolute projection value higher than `cutoffSel(params)` in order to be selected.
`selectionByComp` | The list of components already restricted to the contributing genes

### Details

Selects as feature/gene witness, for each component, the first gene whose absolute projection is greater than a given threshold in at the most `maxNbOcc` components. These witnesses can then be used as representatives of the expression behavior of the contributing genes of the components.

When a feature/gene respecting the given constraints is not found, `maxNbOcc` is incremented of one until a gene is found.

### Value

This function returns a vector of IDs.

### Author(s)

Anne Biton

### Examples

    ## load an example of IcaSet
    data(icaSetCarbayo)

    ## define parameters: features or genes are considered to be contributor
    # when their absolute projection value exceeds a threshold of 4.
    params <- buildMineICAParams(resPath="carbayo/", selCutoff=4)

    ## selection, as gene witnesses, of the genes whose absolute projection is greater than 4
    # in at the most one component. I.e, a gene is selected as a gene witness of a component
    # if he has a large projection on this component only.
    selectWitnessGenes(icaSet=icaSetCarbayo, params=params, level="genes", maxNbOcc=1)

    ## selection, as gene witnesses, of the genes whose absolute projection is greater than 4
    # in at the most two components.
    # I.e, a gene is selected as a gene witness of a given component if he has a large projection
    # in this component and at the most another.
    selectWitnessGenes(icaSet=icaSetCarbayo, params=params, level="genes", maxNbOcc=2)

[Package MineICA version 1.28.0 Index]