class-MineICAParams: Class to contain parameters for the analysis of an ICA...

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

Description

Container for parameters used during the analysis of an ICA decomposition obtained on genomics data.

Creating Objects

new("MineICAParams")

new("MineICAParams", resPath="", genesPath="ProjByComp", pvalCutoff=0.05, selCutoff=3)

Slots

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 (typically expression data) on which the decomposition was calculated.

annotfile

Either a RData or txt file containing the annotation data for the samples (must be of dimensions samples*annotations).

resPath

The path where the outputs of the analysis will be written.

genesPath

The path _within_ the resPath where the gene projections will be written. If missing, will be automatically attributed as resPath/gene2components/.

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 on the absolute feature/gene projection values to consider gene as contributing to a component, 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 use a specific threshold for each component.

Methods

For any slot:

slotName(MineICAParams) and slotName(MineICAParams)<-:

Accessing and setting any slot of name slotName contained in an MineICAParams object.

MineICAParams["slotName"] and MineICAParams["slotName"]<-:

Accessing and setting any slot of name slotName contained in an MineICAParams object.

Author(s)

Anne Biton

See Also

class-MineICAParams, runAn.

Examples

# create an instance of LocSet
new("MineICAParams")

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.