nbOccInComp {MineICA} | R Documentation

## Select components the features contribute to

### Description

For each feature/gene, this function returns the components they contribute to and their projection values across all the components.

### Usage

      nbOccInComp(icaSet, params, selectionByComp = NULL,
        level = c("features", "genes"), file = 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 a threshold on the absolute projections to determine which genes contribute to the components.
`selectionByComp` | The list of components already restricted to the contributing genes
`level` | The attribute of `icaSet` to be used, are reported the occurences of either the `"features"` or the `"genes"`.
`file` | The file where the output data.frame and plots are written.

### Details

A feature/gene is considered as a contributor when its scaled projection value exceeds the threshold `selCutoff(icaSet)`.

This function plots the number of times the feature/gene is a contributor as a function of the standard deviation of its expression profile.

The created files are located in `genePath(params)`. An extensiom '.htm' and '.pdf' is respectively added to the `file` name for the data.frame and the plot outputs.

### Value

Returns a data.frame whose columns are: 'gene' the feature or gene ID, 'nbOcc' the number of components on which the gene contributes according to the threshold, 'components' the indices of these components, and then the component indices which contain its projection values.

### Author(s)

Anne Biton

### Examples

    data(icaSetCarbayo)
    params <- buildMineICAParams(resPath="carbayo/")
    nbOcc <- nbOccInComp(icaSet=icaSetCarbayo, params=params, level="genes", file="gene2MixingMatrix")

[Package MineICA version 1.30.0 Index]