muma: Metabolomics Univariate and Multivariate Analysis
Version 1.4

Preprocessing of high-throughput data (normalization and scalings); Principal Component Analysis with help tool for choosing best-separating principal components and automatic testing for outliers; automatic univariate analysis for parametric and non-parametric data, with generation of specific reports (volcano and box plots); partial least square discriminant analysis (PLS-DA); orthogonal partial least square discriminant analysis (OPLS-DA); Statistical Total Correlation Spectroscopy (STOCSY); Ratio Analysis Nuclear Magnetic Resonance (NMR) Spectroscopy (RANSY).

Browse man pages Browse package API and functions Browse package files

AuthorEdoardo Gaude, Francesca Chignola, Dimitrios Spiliotopoulos, Silvia Mari, Andrea Spitaleri and Michela Ghitti
Date of publication2012-12-03 18:20:37
MaintainerEdoardo gaude <egaude541@gmail.com>
LicenseGPL-2
Version1.4
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("muma")

Man pages

box.plot: Generate box plots
chose.driver: List variables in the dataset
col.pvalues: Color-coding based on significance
explore.data: Preprocessing and principal component analysis of metabolomic...
MetaBc: Metabolomics data of B cells
muma-package: Metabolomics Univariate and Multivariate Analyses
oplsda: Orthogonal Partial Least Sqaure Discriminant Analysis
ostocsy: OSC Statistical TOtal Correlation SpectroscopY
outlier: Test for Outlier
Plot.pca: principal component analysis plotting
Plot.pca.loading: Plot PCA Loading Plot
Plot.pca.pvalues: PCA Loading plot color-coded for univariate significance
Plot.pca.score: Plot PCA Score Plot
Plot.plsda: PLS plots
plsda: Partial Least Square Discriminant Analysis
pvalues: P-values reporting
ransy: Ratio Analysis NMR SpectroscopY
shapiro: Shapiro Wilk's test
stocsy: Statistical TOtal Correlation SpectroscopY
stocsy.1d: Statistical TOtal Correlation SpectroscopY - monodimensional
univariate: Univariate statistical analysis
volcano: Volcano plots
welch: Welch's T test
wmw: Wilcoxon-Mann Whitney U test
work.dir: Create a working directory

Functions

MetaBc Man page
Plot.pca Man page Source code
Plot.pca.loading Man page Source code
Plot.pca.pvalues Man page Source code
Plot.pca.score Man page Source code
Plot.plsda Man page Source code
box.plot Man page Source code
chose.driver Man page Source code
col.pvalues Man page Source code
explore.data Man page Source code
muma Man page
muma-package Man page
oplsda Man page Source code
ostocsy Man page Source code
outlier Man page Source code
plsda Man page Source code
pvalues Man page Source code
ransy Man page Source code
shapiro Man page Source code
stocsy Man page Source code
stocsy.1d Man page Source code
univariate Man page Source code
volcano Man page Source code
welch Man page Source code
wmw Man page Source code
work.dir Man page Source code

Files

MD5
DESCRIPTION
man
man/plsda.Rd
man/pvalues.Rd
man/volcano.Rd
man/stocsy.1d.Rd
man/Plot.pca.Rd
man/ostocsy.Rd
man/shapiro.Rd
man/univariate.Rd
man/wmw.Rd
man/welch.Rd
man/chose.driver.Rd
man/explore.data.Rd
man/muma-package.Rd
man/col.pvalues.Rd
man/Plot.plsda.Rd
man/stocsy.Rd
man/oplsda.Rd
man/MetaBc.Rd
man/ransy.Rd
man/outlier.Rd
man/Plot.pca.pvalues.Rd
man/Plot.pca.score.Rd
man/Plot.pca.loading.Rd
man/box.plot.Rd
man/work.dir.Rd
R
R/Plot.plsda.R
R/outlier.R
R/shapiro.R
R/Plot.pca.pvalues.R
R/box.plot.R
R/plsda.R
R/col.pvalues.R
R/Plot.pca.loading.R
R/oplsda.R
R/Plot.pca.score.R
R/stocsy.1d.R
R/ransy.R
R/univariate.R
R/pvalues.R
R/Plot.pca.R
R/welch.R
R/wmw.R
R/stocsy.R
R/explore.data.R
R/work.dir.R
R/volcano.R
R/ostocsy.R
R/chose.driver.R
NAMESPACE
data
data/MetaBc.rda
muma documentation built on May 19, 2017, 11:28 p.m.