ExposomeSet-class: Class ExposomeSet

Description Usage Arguments Value Methods (by generic) Slots See Also

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

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## 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
)

## 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)

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


rexposome documentation built on March 13, 2021, 2:01 a.m.