MineICAParams:
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.
Examples
Run this code# create an instance of LocSet
new("MineICAParams")
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