ExWAS-class: Class ExWAS

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

Class ExWAS

Description

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 "Exposome-Wide Association Study". The function can be applied to one of to many phenotypes in the ExposomeSet object.

Usage

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

## S4 method for signature 'ExWAS'
extract(object, sort = TRUE, ...)

## S4 method for signature 'ExWAS'
get_robust_sd(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)

Arguments

x	An ExWAS object
y	An ExWAS object
...	NOT USED
object	An object of class ExWAS, mExWAS or nlExWAS.
sort	If TRUE, the results are ordered by pvalue.
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 x-axis
ylab	(optional) Label for y-axis
subtitles	Character vector with the "subtitle" for each plot when given more than one ExWAS.
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 -log10(0.001)) Is the threshold from where the exposures can be taken as significants.
show.effect	(default false) Apply exp to obtained beta.

Value

An object of class ExWAS

Methods (by generic)

• plot(x = ExWAS, y = ANY): Wrapper for plotExwas method.

• extract(ExWAS): Method to obtain the matrix of association scores

• get_robust_sd(ExWAS): Method to obtain the matrix of association scores

• names(ExWAS): Method to obtain the Threshold for effective tests (TEF)

• plotEffect(ExWAS): Draws a plot with the confidence interval of each exposure. Alows to compare two ExWAS instances.

• plotExwas(ExWAS): Method to plot a manhatan plot for association between exposures and phenitypes

• plotVolcano(ExWAS): Method to plot a volcano plot for association between exposures and phenotypes

• tef(ExWAS): Method to obtain the Threshold for effective tests (TEF)

Slots

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).

See Also

exwas to perform an Exposome-Wide Association Study and to create an ExWAS, mexwas to perform a Multivariate Exposome-Wide Association Study and to create a mExWAS

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