MetStaT: Statistical metabolomics tools

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

View on CRAN

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

Files in this package

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

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