Description Usage Arguments Value Methods (by generic) Slots See Also
Class ExWAS
obtained from exwas method of an
ExposomeSet object, contains the result of testing the association
of exposures of an ExposomeSet
to its phenotypes. "ExWAS" is the
acronym of "ExposomeWide Association Study". The function can be applied
to one of to many phenotypes in the ExposomeSet
object.
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  ## S4 method for signature 'ExWAS,ANY'
plot(x, y, ...)
## S4 method for signature 'ExWAS'
extract(object, sort = TRUE, ...)
## S4 method for signature 'ExWAS'
names(x)
## S4 method for signature 'ExWAS'
plotEffect(x, y, select, labels, xlab, ylab)
## S4 method for signature 'ExWAS'
plotExwas(
object,
...,
subtitles,
color,
exp.order,
labels,
show.effective = TRUE
)
## S4 method for signature 'ExWAS'
plotVolcano(x, p.value = log10(0.001), labels, show.effect = FALSE)
## S4 method for signature 'ExWAS'
tef(object)

x 
An 
y 
An 
... 
NOT USED 
object 
An object of class 
sort 
If 
select 
(optional) Vector with the selected exposures 
labels 
(optional) Character vector with the labels for each exposure. It must be labeled vector. 
xlab 
(optional) Label for xaxis 
ylab 
(optional) Label for yaxis 
subtitles 
Character vector with the "subtitle" for each plot when
given more than one 
color 
(optional) A vector of colors. The vector must have length equal to the number of families. The vector must be names with the name of the families. 
exp.order 
(optional) Order of the exposures. 
show.effective 
(default TRUE) draws a brown line on the threshold given by the effective number of tests. 
p.value 
(default 
show.effect 
(default 
An object of class ExWAS
plot
: Wrapper for plotExwas
method.
extract
: Method to obtain the matrix of association scores
names
: Method to obtain the Threshold for effective tests (TEF)
plotEffect
: Draws a plot with the confidence interval of each
exposure. Alows to compare two ExWAS instances.
plotExwas
: Method to plot a manhatan plot for association between
exposures and phenitypes
plotVolcano
: Method to plot a volcano plot for association between
exposures and phenotypes
tef
: Method to obtain the Threshold for effective tests (TEF)
effective
Number containing the effective number of tests.
formula
Tested formula.
comparison
Result of performing the test to find association between levels of exposures and phenotype.
description
Description of the exposures used in the ExWAS. (in description file).
exwas
to perform an ExposomeWide Association Study
and to create an ExWAS
, mexwas
to perform a
Multivariate ExposomeWide Association Study and to create a
mExWAS
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