buildMineICAParams: Creates an object of class MineICAParams

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

Creates an object of class MineICAParams

Description

This function builds an object of class MineICAParams. It contains the parameters that will be used by function runAn to analyze the ICA decomposition contained in an object of class IcaSet.

Usage

  buildMineICAParams(Sfile = new("character"),
    Afile = new("character"), datfile = new("character"),
    annotfile = new("character"), resPath = "", genesPath,
    annot2col = new("character"), pvalCutoff = 0.05,
    selCutoff = 3)

Arguments

Sfile	A txt file containing the Source matrix S.
Afile	A txt file containing the Mixing matrix A.
datfile	A txt file containing the data (e.g expression data) on which the decomposition was calculated.
annotfile	Either a "rda" or "txt" file containing the annotation data for the samples (must be of dimensions samples x annotations).
resPath	The path where the outputs of the analysis will be written, default is the current directory.
genesPath	The path _within_ the resPath where the gene projections will be written. If missing, will be automatically attributed as resPath/ProjByComp/.
annot2col	A vector of colors indexed by annotation levels. If missing, will be automatically attributed using function annot2Color.
pvalCutoff	The cutoff used to consider a p-value significant, default is 0.05.
selCutoff	The cutoff applied to the absolute feature/gene projection values to consider them as contributors, default is 3. Must be either of length 1 and the same treshold is applied to all components, or of length equal to the number of components in order to a specific threshold is for each component.

Value

An object of class MineICAParams

Author(s)

Anne Biton

See Also

MineICAParams, runAn

Examples

## define default parameters and fill resPath
params <- buildMineICAParams(resPath="resMineICACarbayo/")

## change the default cutoff for selection of contribugint genes/features
params <- buildMineICAParams(resPath="resMineICACarbayo/", selCutoff=4)

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