scripts/60a_mixomics.Rnw Version 1
_p_VinskaTrta/_I_EnViRoS/_S_01_Integ/_A_01_Desc-R/
SEEK ID: https://testing.sysmo-db.org/documents/560?version=1
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scripts/60a_mixomics.Rnw
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<<echo=FALSE>>=
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## (c) Andrej Blejec (andrej.blejec@nib.si) ##
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options(width=70)
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\section{Canonical correlation - rCCA}
Dimensionality of the problem requires regularized Canonical correlation analysis (rCCA). We will follow the methods implemented in the package \pkg{mixOmics}. For explanation see \url{http://mixomics.org/methods/rcca/}.
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library(mixOmics)
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Check colinearity of covariance matrices
Metabolites
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covM <- cov(M)
det(covM)
heatmap(covM)
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Transcripts, small submatrix, determinant almost zero
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covT <- cov(T[,sample(1:ncol(T), min(50, ncol(T)))])
det(covT)
heatmap(covT)
@
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Views: 784 Downloads: 41
Created: 7th Nov 2021 at 15:25
Last updated: 7th Nov 2021 at 15:25
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Version 1 (earliest) Created 7th Nov 2021 at 15:25 by Andrej Blejec
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This is a demo project used for the demonstration of R package seekr functionality. R package seekr is based on SEEKR-API and enables batch upload of files organized in pISA-tree structure.
Programme: pISA-tree
Public web page: https://github.com/NIB-SI/seekr
Investigation: _I_EnViRoS Short Name: EnViRoS Title: Integration of data from different platforms Description: * Phenodata: ./phenodata_20201113.txt pISA Investigation creation date: 2020-11-13 pISA Investigation creator: AB Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Studies: Investigation files, _S_01_Integ
Assays: _A_01_Desc-R, _A_02_Upload-R, _I_EnViRoS-files, _S_01_Integ-files
Study: _S_01_Integ Short Name: 01_Integ Title: * Description: * Raw Data: pISA Study creation date: 2020-11-13 pISA Study creator: AB Principal investigator: * License: CC BY 4.0 Sharing permission: Private Upload to FAIRDOMHub: Yes
Submitter: Andrej Blejec
Investigation: _I_EnViRoS | 2021-11-07 16:20:23
Assays: _A_01_Desc-R, _A_02_Upload-R, _S_01_Integ-files
Assay: _A_01_Desc-R Short Name: 01_Desc-R Assay Class: DRY Assay Type: R Title: Data overview and descriptive statistical presentation Description: First we will organize the data and perfom preliminary data analyses to overview what we have. pISA Assay creation date: 2020-11-13 pISA Assay creator: Andrej Blejec Analyst: Andrej Blejec Phenodata: Phenodata_20201109.txt Featuredata: Transcripts1819-02.txt Featuredata metabolites: Featuredata_metabolites_210127.txt Transcript data 18: /input/Transcripts ...
Submitter: Andrej Blejec
Assay type: Experimental Assay Type
Technology type: Technology Type
Investigation: _I_EnViRoS | 2021-11-07 16:20:23
Study: _S_01_Integ
