ExposomePCA-class: Class ExposomePCA

In isglobal-brge/rexposome: Exposome exploration and outcome data analysis

Class ExposomePCA

Description

Class ExposomePCA contains a matrix of exposures used to compute the PCA, also a table of phenotypes and a set congtaing the multiple results of computing the PCA.

Usage

## S4 method for signature 'ExposomePCA,ANY'
plot(x, y, ...)

## S4 method for signature 'ExposomePCA'
exposureNames(object)

## S4 method for signature 'ExposomePCA'
extract(object, table = "exposures", ...)

## S4 method for signature 'ExposomePCA'
ndim(object)

## S4 method for signature 'ExposomePCA'
phenotypeNames(object)

## S4 method for signature 'ExposomePCA'
plot3PCA(
  object,
  cmpX,
  cmpY,
  cmpZ,
  phenotype,
  main,
  angle = 35,
  pch = 16,
  legend = TRUE,
  plines = TRUE
)

## S4 method for signature 'ExposomePCA'
plotEXP(object, exposure)

## S4 method for signature 'ExposomePCA'
plotPCA(
  object,
  set,
  cmpX = 1,
  cmpY = 2,
  show.exposures = FALSE,
  show.samples = FALSE,
  phenotype
)

## S4 method for signature 'ExposomePCA'
plotPHE(object, phenotype, exp2fac = 5)

Arguments

x	Object of class ExposomePCA
y	NOT USED
...	NOT USED
object	An ExposomePCA object
table	Can takes values "exposures" or "individuals".
cmpX	PC to place in X-axis
cmpY	PC to place in Y-axis
cmpZ	PC to place in Z-axis
phenotype	(when set="samples") A phenotype can be selected so the samples are coloured by its value.
main	Title
angle	Point of view
pch	Size of the dots
legend	Boolean to show or hide the legend
plines	Boolean to show of hide the dotted lines that helps to place the dots in the X/Y axes
exposure	Vector of exposures to be shown in the plot
set	Can take values "exposures", "samples" or "all"
show.exposures	When set to TRUE, labels for exposures are shown
show.samples	When set to TRUE, labels for samples are shown
exp2fac	Number of different values to considere an exposures continuous

Value

An object of class ExposomePCA

Methods (by generic)

• plot(x = ExposomePCA, y = ANY): Wrapper for plotPCA method.

• exposureNames(ExposomePCA): Getter to obtain the exposures's names.

• extract(ExposomePCA): Method to extract the raw results of the PCA.

• ndim(ExposomePCA): Number of principal components in an ExposomePCA.

• phenotypeNames(ExposomePCA): Getter to obtain the phenotype's names.

• plot3PCA(ExposomePCA): Methdo to draw a 3D plot for PCA

• plotEXP(ExposomePCA): Plot correlation between exposures and PCA

• plotPCA(ExposomePCA): Methdo to draw a 2D plot for PCA

• plotPHE(ExposomePCA): Plot association score between phentoypes and PCA

Slots

pca

list containing all elements of the PCA

phenoData

Contains the phenotypes or variables experimenter-supplied (see eSet, AnnotatedDataFrame).

featureData

Contains the description of the exposures including the family where they belong (see eSet, AnnotatedDataFrame).

See Also

correlation to study the correlation between exposures in a ExposomeSet

isglobal-brge/rexposome documentation built on Feb. 4, 2023, 12:35 p.m.