MetabolAnalyze: Probabilistic latent variable models for metabolomic data.

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Fits probabilistic principal components analysis, probabilistic principal components and covariates analysis and mixtures of probabilistic principal components models to metabolomic spectral data.

Author
Nyamundanda Gift, Isobel Claire Gormley and Lorraine Brennan.
Date of publication
2012-08-29 14:22:54
Maintainer
Claire Gormley <claire.gormley@ucd.ie>
License
GPL-2
Version
1.3

View on CRAN

Man pages

Aitken
Assess convergence of an EM algorithm.
BrainSpectra
NMR spectral data from brain tissue samples.
estep1
First E step of the AECM algorithm when fitting a mixture of...
estep2
Second E step of the AECM algorithm when fitting a mixture of...
ht
Function to plot a heatmap of BIC values.
loadings.jack.plot
Plot loadings and their associated confidence intervals.
loadings.plot
Plot loadings.
MetabolAnalyze-package
Probabilistic latent variable models for metabolomic data.
mppca.loadings.plot
Plot loadings resulting from fitting a MPPCA model.
mppca.metabol
Fit a mixture of probabilistic principal components analysis...
mppca.scores.plot
Plot scores from a fitted MPPCA model
mstep1
First M-step of the AECM algorithm when fitting a mixture of...
mstep2
Second M-step of the AECM algorithm when fitting a mixture of...
ppca.metabol
Fit a probabilistic principal components analysis (PPCA)...
ppca.metabol.jack
Fit a probabilistic principal components analysis model to a...
ppca.scores.plot
Plot scores from a fitted PPCA model
ppcca.metabol
Fit a probabilistic principal components and covariates...
ppcca.metabol.jack
Fit a probabilistic principal components and covariates...
ppcca.scores.plot
Plot scores from a fitted PPCCA model.
scaling
Function to scale metabolomic spectral data.
standardize
Function to scale covariates.
UrineSpectra
NMR metabolomic spectra from urine samples of 18 mice.

Files in this package

MetabolAnalyze
MetabolAnalyze/MD5
MetabolAnalyze/R
MetabolAnalyze/R/standardize.R
MetabolAnalyze/R/scaling.R
MetabolAnalyze/R/ppcca.scores.plot.R
MetabolAnalyze/R/ppcca.metabol.R
MetabolAnalyze/R/ppcca.metabol.jack.R
MetabolAnalyze/R/ppca.scores.plot.R
MetabolAnalyze/R/ppca.metabol.R
MetabolAnalyze/R/ppca.metabol.jack.R
MetabolAnalyze/R/mstep2.R
MetabolAnalyze/R/mstep1.R
MetabolAnalyze/R/mppca.scores.plot.R
MetabolAnalyze/R/mppca.metabol.R
MetabolAnalyze/R/mppca.loadings.plot.R
MetabolAnalyze/R/loadings.plot.R
MetabolAnalyze/R/loadings.jack.plot.R
MetabolAnalyze/R/ht.R
MetabolAnalyze/R/estep2.R
MetabolAnalyze/R/estep1.R
MetabolAnalyze/R/Aitken.R
MetabolAnalyze/NAMESPACE
MetabolAnalyze/man
MetabolAnalyze/man/UrineSpectra.Rd
MetabolAnalyze/man/standardize.Rd
MetabolAnalyze/man/scaling.Rd
MetabolAnalyze/man/ppcca.scores.plot.Rd
MetabolAnalyze/man/ppcca.metabol.Rd
MetabolAnalyze/man/ppcca.metabol.jack.Rd
MetabolAnalyze/man/ppca.scores.plot.Rd
MetabolAnalyze/man/ppca.metabol.Rd
MetabolAnalyze/man/ppca.metabol.jack.Rd
MetabolAnalyze/man/mstep2.Rd
MetabolAnalyze/man/mstep1.Rd
MetabolAnalyze/man/mppca.scores.plot.Rd
MetabolAnalyze/man/mppca.metabol.Rd
MetabolAnalyze/man/mppca.loadings.plot.Rd
MetabolAnalyze/man/MetabolAnalyze-package.Rd
MetabolAnalyze/man/loadings.plot.Rd
MetabolAnalyze/man/loadings.jack.plot.Rd
MetabolAnalyze/man/ht.Rd
MetabolAnalyze/man/estep2.Rd
MetabolAnalyze/man/estep1.Rd
MetabolAnalyze/man/BrainSpectra.Rd
MetabolAnalyze/man/Aitken.Rd
MetabolAnalyze/inst
MetabolAnalyze/inst/CITATION
MetabolAnalyze/DESCRIPTION
MetabolAnalyze/data
MetabolAnalyze/data/UrineSpectra.rda
MetabolAnalyze/data/BrainSpectra.rda