Function reference • limpca

Package

limpca: Linear modeling of high-dimensional designed data based on ASCA/APCA family of methods

Datasets

UCH: UCH: the Urine Citrate-Hippurate metabolomic dataset

trout: trout: the Rainbow trouts transcriptomic dataset

Data formatting

data2LmpDataList(): Converts data to a lmpDataList.

Data exploration

plotDesign(): Plot of the design matrix

plotLine(): Line plot

plotMeans(): Means plot

plotScatter(): Scatter plot

plotScatterM(): Scatter plot matrix

pcaBySvd(): Singular Value Decomposition for PCA analysis

pcaScreePlot(): Scree Plot

pcaScorePlot(): Score plots

pcaLoading2dPlot(): Loading plots on a 2D scatter plot

pcaLoading1dPlot(): Loadings represented on a line plot.

Modeling

lmpModelMatrix(): Creates the model matrix X

lmpEffectMatrices(): Computes the effect matrices

lmpBootstrapTests(): Tests the significance of model effects by bootstrap.

Effect matrices visualisation

lmpPcaEffects(): PCA on the effect matrices

lmpScreePlot(): Scree Plot

lmpContributions(): Summary of the contributions of each effect

lmpLoading1dPlot(): Loadings represented on a line plot.

lmpLoading2dPlot(): Loading plots on a 2D scatter plot

lmpScorePlot(): Score plots of effect matrices

lmpScoreScatterPlotM(): Scatterplot matrix of effect matrices scores

lmpEffectPlot(): Effect plot