MetStaT: Statistical metabolomics tools

A diverse collection of metabolomics related statistical tools.

Author
Tim Dorscheidt
Date of publication
2013-11-18 10:09:08
Maintainer
Gooitzen Zwanenburg <g.zwanenburg@uva.nl>
License
Apache License (== 2.0)
Version
1.0

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