ExposomePCA-class: Class ExposomePCA

Description Usage Arguments Value Methods (by generic) Slots See Also

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

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## 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)

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


rexposome documentation built on March 13, 2021, 2:01 a.m.