MetStaT: Statistical metabolomics tools
Version 1.0

A diverse collection of metabolomics related statistical tools.

AuthorTim Dorscheidt
Date of publication2013-11-18 10:09:08
MaintainerGooitzen Zwanenburg <g.zwanenburg@uva.nl>
LicenseApache License (== 2.0)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MetStaT")

Popular man pages

ASCA.Calculate: ASCA method (ANOVA-simultaneous component analysis)
ASCAdata: Example data for ASCA.Calculate
ASCA.DoPermutationTest: Permutation test for ASCA
ASCA.GetSummary: Summary method for ASCA analyses
ASCA.Plot: Plot ASCA results
ASCA.PlotScoresPerLevel: ASCA scores plot with projected data.
MetStaT.ExportDataToFile: Exports the results of supplied R expressions as text files...
See all...

All man pages Function index File listing

Man pages

ASCA.Calculate: ASCA method (ANOVA-simultaneous component analysis)
ASCAdata: Example data for ASCA.Calculate
ASCA.DoPermutationTest: Permutation test for ASCA
ASCAF: Indicator matrix for ASCA example.
ASCA.GetPowerSet: Determines the power set of the input set.
ASCA.GetRowRepeats: Determination of all unique row value combinations
ASCA.GetSummary: Summary method for ASCA analyses
ASCA.Plot: Plot ASCA results
ASCA.PlotLoadings: Loadings plot for a specific factor/interaction of the ASCA
ASCA.PlotScores: Score plot for a specific factor or interaction of the ASCA
ASCA.PlotScoresPerLevel: ASCA scores plot with projected data.
ASCAX: Data matrix for ASCA example
FoM.Calculate: Calculate best fitting Figure of Merit using method by Van...
FoMData: Example data for FoM.Calculate
FoM.FitBinnedSampleRepeatErrors: Fitting step in Figure of Merit calculation.
FoM.GetIdOrderedMatrix: Order the matrix of samples by their ID
FoM.OrderAndBinIdByMeans: Bin sample repeats and samples with similar means
MetStaT.ConcatWithStringPars: Concatenates an array of strings
MetStaT.ConvertToNumeric: Converts a matrix of strings to numeric values
MetStaT.ConvertToNumericClasses: Convert value-types in an array or matrix (per column) to...
MetStaT.CreateFileFromHeaderMatrix: Writes a matrix to file with column names and optionally row...
MetStaT.CreateFileFromHeaderRowMatrix: Writes a matrix to file with row and column names, and...
MetStaT.ExportDataToFile: Exports the results of supplied R expressions as text files...
MetStaT.GetFreqTable: Tabulates the frequency of all unique values.
MetStaT.GetPcTuples: Obtain all possible pairs of principal components out of a...
MetStaT.KillAllDevices: Kills all currently active plot windows.
MetStaT.mldivide: Matrix left hand division using a copy of the 'pracma'...
MetStaT.mrdivide: Matrix right hand division using a copy of the 'pracma'...
MetStaT.PlotToFile: Save results of R plotting expressions to files in a zip...
MetStaT.ReadFileToHeaderMatrix: Reads a data file to a matrix.
MetStaT.RemoveNaColumns: Removes all columns in a matrix that contain one or more NAs.
MetStaT.ScalePip: Centering and scaling function
MetStaT.TrimCustom: Limits an input string to a certain length
MetStaT.WriteDataObjectToFile: Write data contained within an R object as character output...
PCA.Calculate: Adapted version of R's base Principal Component Analysis...
PCA.PlotLoadings: Loadings plot for the results of PCA.Calculate
PCA.PlotScores: Score plot for the results of PCA.Calculate.
QStat.Calculate: Global test for metabolic pathway differences between...
QStat.PermutationTest: Accompanying permutation test for QStat.Calculate
QStatX: Data matrix for QStat.Calculate example
QStatY: Matrix for QStat.Calculate example
RevNetJacobian: Example data for RevNetJacobianMethod
RevNet.JacobianMethod: Reverse engineering of networks: Penalized Jacobian method
RevNetTimeLagged: Example data for RevNetTimeLaggedMethod
RevNet.TimeLaggedMethod: Reverse engineering of networks: Time-lagged correlation...
RevNetZeroSlopes: Example data for RevNetZeroSlopesMethod
RevNet.ZeroSlopesMethod: Reverse engineering of networks: zero slopes method
SteadyState: Example data for RevNetJacobianMethod

Functions

Files

inst
inst/MetStaT.pdf
NAMESPACE
data
data/RevNetZeroSlopes.RData
data/FoMData.RData
data/ASCAdata.RData
data/QStat.RData
data/SteadyState.RData
data/RevNetTimeLagged.RData
data/RevNetJacobian.RData
R
R/RevNet.R
R/PCA.R
R/ASCA.R
R/HelperMethods.R
R/Qstat.R
R/FoM.R
MD5
DESCRIPTION
man
man/ASCA.PlotScoresPerLevel.Rd
man/MetStaT.CreateFileFromHeaderRowMatrix.Rd
man/MetStaT.mldivide.Rd
man/FoM.FitBinnedSampleRepeatErrors.Rd
man/FoM.Calculate.Rd
man/RevNetTimeLagged.Rd
man/ASCA.GetPowerSet.Rd
man/ASCAdata.Rd
man/QStat.PermutationTest.Rd
man/ASCA.Calculate.Rd
man/MetStaT.GetPcTuples.Rd
man/MetStaT.ScalePip.Rd
man/PCA.PlotLoadings.Rd
man/MetStaT.ExportDataToFile.Rd
man/MetStaT.WriteDataObjectToFile.Rd
man/MetStaT.RemoveNaColumns.Rd
man/ASCA.GetRowRepeats.Rd
man/MetStaT.ConcatWithStringPars.Rd
man/ASCA.PlotScores.Rd
man/ASCA.GetSummary.Rd
man/MetStaT.ConvertToNumericClasses.Rd
man/MetStaT.KillAllDevices.Rd
man/FoM.GetIdOrderedMatrix.Rd
man/MetStaT.PlotToFile.Rd
man/ASCA.DoPermutationTest.Rd
man/MetStaT.TrimCustom.Rd
man/FoM.OrderAndBinIdByMeans.Rd
man/QStat.Calculate.Rd
man/RevNetJacobian.Rd
man/QStatY.Rd
man/MetStaT.mrdivide.Rd
man/PCA.PlotScores.Rd
man/FoMData.Rd
man/ASCAF.Rd
man/RevNet.TimeLaggedMethod.Rd
man/ASCA.PlotLoadings.Rd
man/QStatX.Rd
man/MetStaT.GetFreqTable.Rd
man/MetStaT.CreateFileFromHeaderMatrix.Rd
man/RevNet.JacobianMethod.Rd
man/RevNet.ZeroSlopesMethod.Rd
man/ASCA.Plot.Rd
man/MetStaT.ConvertToNumeric.Rd
man/PCA.Calculate.Rd
man/ASCAX.Rd
man/RevNetZeroSlopes.Rd
man/MetStaT.ReadFileToHeaderMatrix.Rd
man/SteadyState.Rd
MetStaT documentation built on May 20, 2017, 2:31 a.m.

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