A diverse collection of metabolomics related statistical tools.
Author  Tim Dorscheidt 
Date of publication  20131118 10:09:08 
Maintainer  Gooitzen Zwanenburg <g.zwanenburg@uva.nl> 
License  Apache License (== 2.0) 
Version  1.0 
Package repository  View on CRAN 
Installation  Install the latest version of this package by entering the following in R:

All man pages Function index File listing
Man pages  

ASCA.Calculate: ASCA method (ANOVAsimultaneous 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 valuetypes 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: Timelagged 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 
Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.
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