buildMineICAParams: Creates an object of class MineICAParams

Description Usage Arguments Value Author(s) See Also Examples

View source: R/functions.R

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

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  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

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## 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)

Bioconductor-mirror/MineICA documentation built on May 29, 2017, 8:30 a.m.