![]() Number of principal components to calculate. Svd PCA is chosen for data wihout missing values and Numberic variables are used to fit the PCA. Can also be a data frame in which case all Also takesĮxpressionSet in which case the transposed expression Such) with samples in rows and variables as columns. Numerical matrix with (or an object coercible to Pca ( object, method, nPcs = 2, scale = c ( "none", "pareto", "vector", "uv" ), center = TRUE, completeObs = TRUE, subset = NULL, cv = c ( "none", "q2" ). plot.pcaRes: Plot diagnostics (screeplot).pcaRes: Class for representing a PCA result.pcaNet: Class representation of the NLPCA neural net.pcaMethods-deprecated: Deprecated methods for pcaMethods.pca: Perform principal component analysis.optiAlgCgd: Conjugate gradient optimization.nVar-pcaRes-method: Get the number of variables used to build the PCA model.nObs-pcaRes-method: Get the number of observations used to build the PCA model.nniRes: Class for representing a nearest neighbour imputation result.method-pcaRes-method: Get the used PCA method.metaboliteDataComplete: A complete metabolite data set from an Arabidopsis coldstress.metaboliteData: A incomplete metabolite data set from an Arabidopsis.loadings-pcaRes-method: Get loadings from a pcaRes object.loadings.pcaRes: Get loadings from a pcaRes object.loadings-ANY-method: Crude way to unmask the function with the same name from.lineSearch: Line search for conjugate gradient.leverage-pcaRes-method: Extract leverages of a PCA model.kEstimateFast: Estimate best number of Components for missing value.kEstimate: Estimate best number of Components for missing value.forkNlpcaNet: Complete copy of nlpca net object.fitted-methods: Extract fitted values from PCA.cvstat-pcaRes-method: Get cross-validation statistics (e.g.completeObs-nniRes-method: Get the original data with missing values replaced with.checkData: Do some basic checks on a given data matrix.center-pcaRes-method: Get the centers of the original variables.centered-pcaRes-method: Check centering was part of the model. ![]() bpca: Bayesian PCA missing value estimation.biplot-methods: Plot a overlaid scores and loadings plot.asExprSet: Convert pcaRes object to an expression set.
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