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

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

Class to contain parameters for the analysis of an ICA decomposition.

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")

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