selectWitnessGenes: selectWitnessGenes

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

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)

bitona/MineICA documentation built on April 23, 2023, 1:41 p.m.