Description Usage Arguments Value Methods (by generic) Slots See Also
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45  ## 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)

x 
Object of class 
y 
NOT USED 
... 
NOT USED 
object 
An 
table 
Can takes values 
cmpX 
PC to place in Xaxis 
cmpY 
PC to place in Yaxis 
cmpZ 
PC to place in Zaxis 
phenotype 
(when 
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 
show.exposures 
When set to 
show.samples 
When set to 
exp2fac 
Number of different values to considere an exposures continuous 
An object of class ExposomePCA
plot
: Wrapper for plotPCA
method.
exposureNames
: Getter to obtain the exposures's names.
extract
: Method to extract the raw results of the PCA.
ndim
: Number of principal components in an ExposomePCA.
phenotypeNames
: Getter to obtain the phenotype's names.
plot3PCA
: Methdo to draw a 3D plot for PCA
plotEXP
: Plot correlation between exposures and PCA
plotPCA
: Methdo to draw a 2D plot for PCA
plotPHE
: Plot association score between phentoypes and PCA
pca
list containing all elements of the PCA
phenoData
Contains the phenotypes or variables experimentersupplied (see eSet, AnnotatedDataFrame).
featureData
Contains the description of the exposures including the family where they belong (see eSet, AnnotatedDataFrame).
correlation
to study the correlation between
exposures in a ExposomeSet
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