PCA {NOISeq} | R Documentation |
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.
## S4 method for signature 'PCA' explo.plot(object, samples = 1:2, plottype = "scores", factor = NULL) ## S4 method for signature 'PCA' dat2save(object)
object |
Object generated from |
samples |
Principal components to be plotted. If NULL, the two first components are plotted. |
plottype |
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. |
factor |
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 dat2save
method
to save the relevant information in an object cleanly. It also has an
explo.plot
method to plot the data contained in the object.
Sonia Tarazona