ExposomeSet-class: Class ExposomeSet

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

Class ExposomeSet

Description

Class ExposomeSet contains the exposure levels, the exposure's description and the samples phenotype. It is the starting object for rexposome package and extends eSet.

Usage

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

## S4 method for signature 'ExposomeSet'
clustering(object, method, cmethod, ..., warnings = TRUE)

## S4 method for signature 'ExposomeSet'
correlation(object, ..., warnings = TRUE)

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

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

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

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

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

## S4 method for signature 'ExposomeSet'
highAndLow(
  object,
  ngroups = 3,
  intervals = c("standard", "extreme"),
  select,
  drop = FALSE,
  warnings = TRUE
)

## S4 method for signature 'ExposomeSet'
ilod(
  object,
  seed = 1234,
  lod.col = "LOD",
  pNA = 0.2,
  tLog = FALSE,
  method = "QRILC",
  warnings = TRUE,
  ...
)

## S4 method for signature 'ExposomeSet'
imputation(object, select, ..., messages = FALSE)

## S4 method for signature 'ExposomeSet'
invExWAS(object, formula, filter, tef = TRUE, verbose = FALSE, warnings = TRUE)

## S4 method for signature 'ExposomeSet'
mexwas(object, phenotype, family, warnings = TRUE)

## S4 method for signature 'ExposomeSet'
normalityTest(
  object,
  exposure,
  th = 0.05,
  min.val = 5,
  na.rm = TRUE,
  warnings = TRUE
)

## S4 method for signature 'ExposomeSet'
pca(object, npc = 10, pca = FALSE, ...)

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

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

## S4 method for signature 'ExposomeSet'
plotHistogram(x, select, density = TRUE, show.trans = FALSE)

## S4 method for signature 'ExposomeSet'
plotLOD(object, lod.col = "LOD", x.max = 100, sort = TRUE)

## S4 method for signature 'ExposomeSet'
plotMissings(
  object,
  set = c("exposures", "phenotypes"),
  x.max = 100,
  sort = TRUE
)

## S4 method for signature 'ExposomeSet'
standardize(object, select, method = "normal", na.rm = TRUE, warnings = TRUE)

## S4 method for signature 'ExposomeSet'
Summary(x, set = c("exposures", "phenotypes"), select, ..., na.rm = FALSE)

## S4 method for signature 'ExposomeSet'
tableLOD(object, output = "n", lod.col = "LOD", sort = TRUE)

## S4 method for signature 'ExposomeSet'
tableMissings(
  object,
  set = c("exposures", "phenotypes"),
  output = "n",
  sort = TRUE
)

## S4 method for signature 'ExposomeSet'
trans(object, fun, select, by.exposure = FALSE, ...)

Arguments

x	An ExposomeSet object.
y	NOT USED
...	Arguments to be passed to imputeFAMD
object	An ExposomeSet object.
method	Method to be used.
cmethod	Function implementing a systsme to retrieve classification from clustering output
warnings	If set to TRUE it prints the warning messsages.
formula	Formula, not including exposures, to be tested. No need to provide response (left term)
filter	Expression to be used to filter ExposomeSet
family	Family descriving the nature of the health outcome
baselevels	Labeled vector with the default base level for categorical exposures.
tef	If TRUE it computed the threshold for effective tests.
verbose	If set to TRUE is shows messages on progression.
by.exposure	If set to TRUE ir returns the family which each exposure belongs
ngroups	Number of intervals to be used
intervals	If "standard" all levels are kept, if "extreme" intermetiate levels are set to NA.
select	Vector selecting thee xposures to be used.
drop	If set to TRUE exposures are replaced
seed	Numeric seed
lod.col	Indicator of the column where the LOD is located
pNA	Maximum percentage allowed of values under LOD
tLog	If set to TRUE it transforms all the exposures to lod before the imputation.
messages	If set to TRUE messages from mice's function will be displayed.
phenotype	Health outcome to be used as dependent variable.
exposure	Vecror of exposures to be used.
th	Threshold of P-Value used to considere normalit
min.val	Minimum number of observations to perform test
na.rm	If set to TRUE removes NA values
npc	Number of PC to be kept
pca	Perform PCA (only numerical variables) or FAMD (numerical and categorical)
group	Phenotype to group exposures
group2	Phenotype to group exposures
scatter	If set to true it shows the samples value in the plot
na.omit	If set to TRUE, NA values are discarded
density	If set to TRUE a desntiry plot is draw on the histogram
show.trans	If set to TRUE, three extra plots are drawn with usual transformations
x.max	Threshold for x axis (in %)
sort	If set to TRUE, results are ordered
set	Cantake values "exposures" or "phentoypes".
output	Can take values "n" (count) ot "p" (percentage)
fun	Function to bt used in the transformation process

Value

An object of class ExposomeSet

Methods (by generic)

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

• clustering(ExposomeSet): Performs clustering on samples based on exposure levels.

• correlation(ExposomeSet): Computes correlation on exposures.

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

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

• exposureNames(ExposomeSet): Getter to obtain the exposures's names.

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

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

• highAndLow(ExposomeSet): Performs a discretization of continuous exposures.

• ilod(ExposomeSet): Imputation of under-LOD values of exposures.

• imputation(ExposomeSet): Imputation of missing values of exposures.

• invExWAS(ExposomeSet): Performs an EXposome-Wide Association Study (modelling the exposures as response)

• mexwas(ExposomeSet): Performs a Multiple-EXposure-Wide Association Study.

• normalityTest(ExposomeSet): Test the normality of each exposure.

• pca(ExposomeSet): Performs a PCA

• phenotypeNames(ExposomeSet): Getter to obtain the phenotypes's names.

• plotFamily(ExposomeSet): Draws a boxplot or accumulated-bar plot for each exposure in a given family.

• plotHistogram(ExposomeSet): Draws an histogram of a given continuous exposure or a pie chart if a given categorycal exposure.

• plotLOD(ExposomeSet): Draws a barchart with the amount of under-LOD values.

• plotMissings(ExposomeSet): Draws a bar-plot with the amount of missing values.

• standardize(ExposomeSet): Standardization of exposures.

• Summary(ExposomeSet): Summary of both continuous and categorical exposures

• tableLOD(ExposomeSet): Returns a vector with the number of under-LOD values per exposure.

• tableMissings(ExposomeSet): Returns a vector with the number of missing values per exposure.

• trans(ExposomeSet): Transformation of exposures.

Slots

assayData

Contains the exposures matrix with column number equal to nrow(phenoData) (see eSet, AssayData).

featureData

Contains the description of the exposures including the family where they belong (see eSet, AnnotatedDataFrame).

phenoData

Contains the phenotypes or variables experimenter-supplied (see eSet, AnnotatedDataFrame).

See Also

readExposome to create an ExposomeSet from files, loadExposome to create an ExposomeSet from data.frames

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