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Last data update: 2014.03.03

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Classification

Results 1 - 10 of 27 found.
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caClass-class (Package: STATegRa) : caClass

Stores the results of any of the omicsPCA analyses.

● Data Source: BioConductor
● Keywords:
● Alias: caClass-class
● 0 images

createOmicsExpressionSet (Package: STATegRa) : createOmicsExpressionSet

This function allow to the user to create a ExpressionSet object from a matrix representing an omics dataset. It allows to include the experimental design and annotation in the ExpressionSet object.

● Data Source: BioConductor
● Keywords: datagen
● Alias: createOmicsExpressionSet, createOmicsExpressionSet,matrix-method
● 0 images

getInitialData (Package: STATegRa) : Retrieve initial data from caClass objects

Generic function to retrieve the initial data used for by omicsCompAnalysis from a caClass-class object

● Data Source: BioConductor
● Keywords:
● Alias: getInitialData, getInitialData,caClass-method
● 0 images

getLoadings (Package: STATegRa) : Retrieve component analysis loadings

Generic function to retrieve loadings (common and distinctive) found by omicsCompAnalysis on a caClass-class object.

● Data Source: BioConductor
● Keywords:
● Alias: getLoadings, getLoadings,caClass-method
● 0 images

getMethodInfo (Package: STATegRa) : Retrieve information about component analysis method

Generic function to retrieve information about the method used by omicsCompAnalysis on a caClass-class object.

● Data Source: BioConductor
● Keywords:
● Alias: getMethodInfo, getMethodInfo,caClass-method
● 0 images

getPreprocessing (Package: STATegRa) : Retrieve information about preprocessing

Generic function to retrieve information about the preprocessing done by omicsCompAnalysis on a caClass-class object.

● Data Source: BioConductor
● Keywords:
● Alias: getPreprocessing, getPreprocessing,caClass-method
● 0 images

getScores (Package: STATegRa) : Retrieve component analysis scores

Generic function to retrieve scores (common and distinctive) found by omicsCompAnalysis on a caClass-class object.

● Data Source: BioConductor
● Keywords:
● Alias: getScores, getScores,caClass-method
● 0 images

getVAF (Package: STATegRa) : Retrieve information abotut VAF

Generic function to retrieve VAF found by omicsCompAnalysis on a caClass-class object.

● Data Source: BioConductor
● Keywords:
● Alias: getVAF, getVAF,caClass-method
● 0 images

holistOmics (Package: STATegRa) : HolistOmics an application of NPC on omics datasets

This function applies the NonParametric Combination methodology on the integrative analysis of different omics data modalities. It retrieves diffential expressed genes between control and treatment, taking into account all omics data. First, each datatype is analyzed independently using the appropriate method. HolistOmics analyses static (one time point) RNAseq, using Voom+limma method, and static (one time point) Microarray, using limma. Then, the resulting p-values are combined employing Fisher, Liptak and Tippett combining functions. Tippett function returns findings which are supported by at least one omics modality. Liptak function returns findings which are supportd by most modalities. Fisher function has an intermediate behavior between those of Tippett and Liptak.

● Data Source: BioConductor
● Keywords:
● Alias: holistOmics, holistOmics,list,character-method
● 0 images

modelSelection (Package: STATegRa) : Find optimal common and distinctive components

Uses selectCommonComps and PCA.selection to estimate the optimal number of common and distinctive components according to given selection criteria.

● Data Source: BioConductor
● Keywords:
● Alias: modelSelection, modelSelection,list,numeric,character-method
● 0 images