nbOccInComp_simple: nbOccInComp_simple

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

nbOccInComp_simple

Description

For each feature/gene, this function returns the indices of the components they contribute to.

Usage

  nbOccInComp_simple(icaSet, params,
    selectionByComp = NULL, level = c("features", "genes"))

Arguments

icaSet	An object of class IcaSet.
params	An object of class MineICAParams containing the parameters of the analysis. cutoffSel(params) is used as a threshold on the absolute projections to select the contributing features/genes.
selectionByComp	The list of components already restricted to the contributing features/genes (each element is a vector of projection values indexed by features or genes).
level	The attribute of icaSet to be used, the occurences of either the "features" (using S(icaSet)) or the "genes" (using SByGene(icaSet)) will be reported.

Value

Returns a data.frame whose columns are: gene the feature or gene IDs, nbOcc the number of components the gene contributes to, components the indices of those components.

Author(s)

Anne Biton

Examples

data(icaSetCarbayo)
params <- buildMineICAParams(resPath="carbayo/")
nbOcc <- MineICA:::nbOccInComp_simple(icaSet=icaSetCarbayo, params=params, level="genes")

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