PCA: PCA class

In SoniaTC/NOISeq: Exploratory analysis and differential expression for RNA-seq data

Description

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.

Usage

## S4 method for signature 'PCA'
explo.plot(object, samples = 1:2, plottype = "scores", factor = NULL)
## S4 method for signature 'PCA'
dat2save(object)

Arguments

object	Object generated from dat() function.
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.

Slots/List Components

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".

Methods

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.

Author(s)

Sonia Tarazona

SoniaTC/NOISeq documentation built on July 28, 2020, 6:31 p.m.