PCA class generated from dat() function with type="PCA". This object contains the results of the PCA on the data matrix as well as the arguments used.
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Object generated from
Principal components to be plotted. If NULL, the two first components are plotted.
If plottype="scores", the experimental samples are displayed in the plot and colored according to the values of the selected factor. If plottype="loadings", the genes are plotted.
The samples in the score plot will be colored according to the values of the selected factor. If NULL, the first factor is chosen.
An object of this class contains an element (dat) which is a list with the following components:
result: List containing the output of PCA. It contains the following elements: "eigen" (eigenvalues and eigenvectors from the PCA decomposition),
"var.exp" (variance explained by each Principal Component), "scores" (coefficients of samples in each PC), "loadings" (coefficients of genes in each PC).
factors: Data.frame with factors inherited from object generated by readData() function.
norm: Value provided for argument "norm".
logtransf: Value provided for argument "logtransf".
This class has an specific
show method in order to work and print
a summary of the elements which are contained and a
to save the relevant information in an object cleanly. It also has an
explo.plot method to plot the data contained in the object.
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