imExposomeSet-class: Class imExposomeSet

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

Class imExposomeSet

Description

Class imExposomeSet was designed to store the exposures obtained after a multiple imputation process done using mice. The data.frame obtained from mice has the particulatiry to contain the columns .imp and .id joint to phenotypes and exposures. The slots assayData, featureData, and phenoData are coordinated.

Usage

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

## S4 method for signature 'imExposomeSet'
dim(x)

## S4 method for signature 'imExposomeSet'
expos(object)

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

## S4 method for signature 'imExposomeSet'
extract(object, rid = -1, ...)

## S4 method for signature 'imExposomeSet'
exwas(
  object,
  formula,
  filter,
  family,
  ...,
  baselevels,
  tef = TRUE,
  verbose = FALSE,
  warnings = TRUE,
  robust = FALSE
)

## S4 method for signature 'imExposomeSet'
familyNames(object, by.exposure = FALSE)

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

## S4 method for signature 'imExposomeSet'
plotFamily(x, family, group, group2, scatter = FALSE, na.omit = TRUE)

## S4 method for signature 'imExposomeSet'
sampleNames(object)

## S4 method for signature 'imExposomeSet'
x[[i]]

## S4 method for signature 'imExposomeSet,ANY,ANY,ANY'
x[i, j, k, ..., drop = FALSE]

## S4 method for signature 'imExposomeSet'
toES(object, rid = 1)

Arguments

x	An imExposomeSet object.
y	NOT USED
...	Other used arguments
object	An object of class imExposomeSet
rid	Number of the imputation to be extracted
formula	Formula, not including exposures, to be tested.
filter	Expression to be used to filter ExposomeSet
family	Family descriving the nature of the health outcome
baselevels	Labeled vector with the base-level of the categorical exposures
tef	If set to TRUE the threshold for effective test is computed.
verbose	If set to TRUE it shows messages on progression.
warnings	If set to TRUE it shows warnings on progession.
by.exposure	If set to TRUE ir returns the family which each exposure belongs
group	Phenotype to group exposures
group2	NOT USED
scatter	If set to true it shows the samples value in the plot
na.omit	NOT USED
i	Character coresponding to selected exposures.
j	Character corresponding to selected sample names.
k	Character corresponding to selected phenotypes.
drop	NOT USED

Value

An object of class imExposomeSet

Methods (by generic)

• plot(x = imExposomeSet, y = ANY): Wrapper for plotFamily method.

• dim(imExposomeSet): Returns the number of exsures, samples and phenotypes.

• expos(imExposomeSet): Returns a data.frame with exposures.

• exposureNames(imExposomeSet): Method to obtain samples' names

• extract(imExposomeSet): Method to extract exposures for a single imputation

• exwas(imExposomeSet): Performs an EXposome-Wide Association Study

• familyNames(imExposomeSet): Getter to obtain the families's names of the family of each exposure.

• phenotypeNames(imExposomeSet): Getter to obtain the families's names of the family of each exposure.

• plotFamily(imExposomeSet): Draws a boxplot or accumulated-bar plot for each exposure in the all imputed sets.

• sampleNames(imExposomeSet): Method to obtain samples' names

• [[: Get an ExposomeSet with the selected imputation

• x[i: Subset an imExposomeSet

• toES(imExposomeSet): Returns an ExposomeSet with ethe given imputation.

Slots

nimputation

Number of imputations done with mice.

assayData

data.frame containing .imp, .id and the exposures.

featureData

data.frame containing the description of the exposures.

phenoData

data.frame containing .imp, .id and the phenotypes.

Note

Sample order is not guarantee

See Also

loadImputed to create an imExposomeSet from data.frames

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