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

Functions

ASCAdata Man page
ASCA.DoPermutationTest Man page
ASCAF Man page
ASCA.GetPowerSet Man page
ASCA.GetRowRepeats Man page
ASCA.GetSummary Man page
ASCA.Plot Man page
ASCA.PlotLoadings Man page
ASCA.PlotScores Man page
ASCA.PlotScoresPerLevel Man page
ASCAX Man page
FoM.Calculate Man page
FoMData Man page
FoM.FitBinnedSampleRepeatErrors Man page
FoM.GetIdOrderedMatrix Man page
FoM.OrderAndBinIdByMeans Man page
MetStaT.ConcatWithStringPars Man page
MetStaT.ConvertToNumeric Man page
MetStaT.ConvertToNumericClasses Man page
MetStaT.CreateFileFromHeaderMatrix Man page
MetStaT.CreateFileFromHeaderRowMatrix Man page
MetStaT.ExportDataToFile Man page
MetStaT.GetFreqTable Man page
MetStaT.GetPcTuples Man page
MetStaT.KillAllDevices Man page
MetStaT.mldivide Man page
MetStaT.mrdivide Man page
MetStaT.PlotToFile Man page
MetStaT.ReadFileToHeaderMatrix Man page
MetStaT.RemoveNaColumns Man page
MetStaT.ScalePip Man page
MetStaT.TrimCustom Man page
MetStaT.WriteDataObjectToFile Man page
PCA.Calculate Man page
PCA.PlotLoadings Man page
PCA.PlotScores Man page
QStat.Calculate Man page
QStat.PermutationTest Man page
QStatX Man page
QStatY Man page
RevNetJacobian Man page
RevNet.JacobianMethod Man page
RevNetTimeLagged Man page
RevNet.TimeLaggedMethod Man page
RevNetZeroSlopes Man page
RevNet.ZeroSlopesMethod Man page
SteadyState Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.