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MetStaT (version 1.0)
Statistical metabolomics tools
Description
A diverse collection of metabolomics related statistical tools.
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Version
Version
1.0
Install
install.packages('MetStaT')
Monthly Downloads
8
Version
1.0
License
Apache License (== 2.0)
Maintainer
Gooitzen Zwanenburg
Last Published
November 18th, 2013
Functions in MetStaT (1.0)
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ASCAF
Indicator matrix for ASCA example.
FoM.FitBinnedSampleRepeatErrors
Fitting step in Figure of Merit calculation.
FoM.GetIdOrderedMatrix
Order the matrix of samples by their ID
ASCA.PlotScores
Score plot for a specific factor or interaction of the ASCA
ASCA.PlotLoadings
Loadings plot for a specific factor/interaction of the ASCA
MetStaT.ConvertToNumericClasses
Convert value-types in an array or matrix (per column) to pre-defined class-values
ASCA.GetPowerSet
Determines the power set of the input set.
MetStaT.GetPcTuples
Obtain all possible pairs of principal components out of a defined set.
ASCA.GetRowRepeats
Determination of all unique row value combinations
RevNet.ZeroSlopesMethod
Reverse engineering of networks: zero slopes method
MetStaT.KillAllDevices
Kills all currently active plot windows.
MetStaT.ReadFileToHeaderMatrix
Reads a data file to a matrix.
QStat.PermutationTest
Accompanying permutation test for QStat.Calculate
PCA.PlotScores
Score plot for the results of PCA.Calculate.
RevNetZeroSlopes
Example data for RevNetZeroSlopesMethod
MetStaT.mrdivide
Matrix right hand division using a copy of the 'pracma' package 'mrdivide' method.
PCA.Calculate
Adapted version of R's base Principal Component Analysis function (svd)
RevNetTimeLagged
Example data for RevNetTimeLaggedMethod
MetStaT.GetFreqTable
Tabulates the frequency of all unique values.
RevNet.JacobianMethod
Reverse engineering of networks: Penalized Jacobian method
MetStaT.ScalePip
Centering and scaling function
MetStaT.ExportDataToFile
Exports the results of supplied R expressions as text files in a single zip package.
SteadyState
Example data for RevNetJacobianMethod
QStatY
Matrix for QStat.Calculate example
MetStaT.RemoveNaColumns
Removes all columns in a matrix that contain one or more NAs.
MetStaT.ConvertToNumeric
Converts a matrix of strings to numeric values
MetStaT.TrimCustom
Limits an input string to a certain length
MetStaT.CreateFileFromHeaderRowMatrix
Writes a matrix to file with row and column names, and optionally a description at the first (top left) data position in the file.
RevNet.TimeLaggedMethod
Reverse engineering of networks: Time-lagged correlation method
MetStaT.CreateFileFromHeaderMatrix
Writes a matrix to file with column names and optionally row names as well.
ASCAdata
Example data for ASCA.Calculate
ASCA.PlotScoresPerLevel
ASCA scores plot with projected data.
ASCA.Calculate
ASCA method (ANOVA-simultaneous component analysis)
ASCA.DoPermutationTest
Permutation test for ASCA
ASCA.GetSummary
Summary method for ASCA analyses
ASCAX
Data matrix for ASCA example
FoM.OrderAndBinIdByMeans
Bin sample repeats and samples with similar means
FoMData
Example data for FoM.Calculate
FoM.Calculate
Calculate best fitting Figure of Merit using method by Van Batenburg et al. (2011).
ASCA.Plot
Plot ASCA results
QStatX
Data matrix for QStat.Calculate example
RevNetJacobian
Example data for RevNetJacobianMethod
QStat.Calculate
Global test for metabolic pathway differences between conditions
MetStaT.ConcatWithStringPars
Concatenates an array of strings
MetStaT.PlotToFile
Save results of R plotting expressions to files in a zip package.
PCA.PlotLoadings
Loadings plot for the results of PCA.Calculate
MetStaT.WriteDataObjectToFile
Write data contained within an R object as character output to a file.
MetStaT.mldivide
Matrix left hand division using a copy of the 'pracma' package 'mldivide' method.
ASCA.Calculate
ASCA method (ANOVA-simultaneous component analysis)