selectWitnessGenes: selectWitnessGenes
In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description Usage Arguments Details Value Author(s) Examples

This function selects a gene per component.

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

`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

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.

This function returns a vector of IDs.

Anne Biton

## 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)