# Exposome exploration and outcome data analysis

## Documentation for package ‘rexposome’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

C D E F G H I L M N P R S T V misc

## -- C --

classification | Method to get the classification of the samples from an ExposomeClust.
classification-method | Class ExposomeClust
clustering | Method to perform clustering on the samples of an ExposomeSet
clustering-method | Class ExposomeSet
correlation | Creation of an ExposomeCorr from an ExposomeSet.
correlation-method | Class ExposomeSet

## -- D --

dim-method | Class ExposomeCorr
dim-method | Class ExposomeSet
dim-method | Class imExposomeSet

## -- E --

expo | 'ExposomeSet' for testing purpouses
expos | Returns the exposures matrix of an ExposomeSet.
expos-method | Class ExposomeSet
expos-method | Class imExposomeSet
ExposomeClust | Class ExposomeClust
ExposomeClust-class | Class ExposomeClust
ExposomeCorr | Class ExposomeCorr
ExposomeCorr-class | Class ExposomeCorr
ExposomePCA | Class ExposomePCA
ExposomePCA-class | Class ExposomePCA
ExposomeSet | Class ExposomeSet
ExposomeSet-class | Class ExposomeSet
exposureNames | Getter to obtain the exposures's names of an ExposomeSet or ExposomePCA
exposureNames-method | Class ExposomePCA
exposureNames-method | Class ExposomeSet
exposureNames-method | Class imExposomeSet
expo_c | 'ExposomeClust' for testing purpouses
extract | Raw data from 'ExWAS', 'ExposomeClust' and 'ExposomeCorr'.
extract | Raw data from 'ExWAS'
extract-method | Class ExWAS
extract-method | Class ExposomeCorr
extract-method | Class ExposomePCA
extract-method | Class imExposomeSet
extract-method | Class mExWAS
ExWAS | Class ExWAS
exwas | Testing the association between an exposure and a phenotype of an ExposomeSet
ExWAS-class | Class ExWAS
exwas-method | Class ExposomeSet
exwas-method | Class imExposomeSet
ex_imp | 'imExposomeSet' for testing purpouses

## -- F --

familyNames | Getter to obtain the exposures's names of an ExposomeSet.
familyNames-method | Class ExposomeSet
familyNames-method | Class imExposomeSet

## -- G --

get_robust_sd | Raw data from 'ExWAS'
get_robust_sd-method | Class ExWAS

## -- H --

highAndLow | Function to convert continuous exposures to categorical exposures
highAndLow-method | Class ExposomeSet

## -- I --

ilod | Function to impute under-LOD values from an ExposomeSet
ilod-method | Class ExposomeSet
imExposomeSet | Class imExposomeSet
imExposomeSet-class | Class imExposomeSet
imExposomeSet-methods | Class imExposomeSet
imputation | Function to impute missing values from an ExposomeSet
imputation-method | Class ExposomeSet
imputeLOD | Function to impute values under limit of detection
invExWAS | Testing the association between an exposure and a phenotype of an ExposomeSet (modelling the exposures as response)
invExWAS-method | Class ExposomeSet

## -- L --

loadExposome | Creation of an ExposomeSet from 'data.frames'
loadExposome_plain | Creation of an ExposomeSet from single 'data.frame'
loadImputed | Creation of an imExposomeSet from 'data.frames'

## -- M --

me | 'data.frame' for testing purpouses
mExWAS | Class mExWAS
mexwas | Testing the association between an exposure and a phenotype of an ExposomeSet using a multivariate aproach.
mExWAS-class | Class mExWAS
mexwas-method | Class ExposomeSet

## -- N --

names-method | Class ExWAS
ndim | Number of principal components in an ExposomePCA.
ndim-method | Class ExposomePCA
normalityTest | It creates a 'data.frame' of boolean indicating if the exposures follows a normal distribution or not.
normalityTest-method | Class ExposomeSet

## -- P --

pca | Creation of an ExposomePCA from an ExposomeSet.
pca-method | Class ExposomeSet
phenotypeNames | Getter to obtain the phenotype's names of an ExposomeSet or ExposomePCA.
phenotypeNames-method | Class ExposomePCA
phenotypeNames-method | Class ExposomeSet
phenotypeNames-method | Class imExposomeSet
plot-method | Class ExWAS
plot-method | Class ExposomeClust
plot-method | Class ExposomeCorr
plot-method | Class ExposomePCA
plot-method | Class ExposomeSet
plot-method | Class imExposomeSet
plot-method | Class mExWAS
plot3PCA | Ploting PCA in a 3D space
plot3PCA-method | Class ExposomePCA
plotClassification | Draw the profile of the levels exposures after a classification with a clustering method
plotClassification-method | Class ExposomeClust
plotCorrelation | It draws both circos or matrix plot for the correlation in ExposomeCorr
plotCorrelation-method | Class ExposomeCorr
plotEffect | Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotEffect-method | Class ExWAS
plotEXP | Plot correlation between exposures and PCA
plotEXP-method | Class ExposomePCA
plotExwas | Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotExwas-method | Class ExWAS
plotExwas-method | Class mExWAS
plotFamily | It draws the profile of the exposome in an ExposomeSet
plotFamily-method | Class ExposomeSet
plotFamily-method | Class imExposomeSet
plotHistogram | It draws a histogram for each exposure in an ExposomeSet
plotHistogram-method | Class ExposomeSet
plotLOD | It draws a chart with the percentage of under-LOD values in an ExposomeSet
plotLOD-method | Class ExposomeSet
plotMissings | It draws a chart with the percentage of missing in an ExposomeSet
plotMissings-method | Class ExposomeSet
plotPCA | Ploting PCA
plotPCA-method | Class ExposomePCA
plotPHE | Plot association score between phentoypes and PCA
plotPHE-method | Class ExposomePCA
plotVolcano | Function to draw a plot of the pvalues stored in an 'ExWAS' object
plotVolcano-method | Class ExWAS

## -- R --

readExposome | Creation of an ExposomeSet from files
rexposome | rexposome: Package for exposome exploration and outcome data analysis

## -- S --

sampleNames-method | Class ExposomeClust
sampleNames-method | Class imExposomeSet

standardize

#' Summary of an ExposomeSet. #' #' Given an ExposomeSet is shows a summary for its exposures or #' its phenotypes. #' #' @name Summary #' @rdname Summary-methods #' @aliases Summary #' @param object codeExposomeSet with 'set' will be summarized. #' @param set Set to be sumarized ('"exposures"' or '"phenotypes"'). #' @param select Subseting of exposures of phenotypes. #' @return A basic description of the exposures in the 'ExposomeSet' #' @examples #' data("exposome") #' Summary(expo, set = "exposures") #' @export Summary setGeneric("Summary", function(object, set=c("exposures", "phenotypes"), select) standardGeneric("Summary") ) Standardize of an ExposomeSet.

standardize-method | Class ExposomeSet
Summary-method | Class ExposomeSet

## -- T --

tableLOD | It creates a vector with the amount of under-LOD exposures in an ExposomeSet
tableLOD-method | Class ExposomeSet
tableMissings | It creates a vector with the amount of missing in an ExposomeSet
tableMissings-method | Class ExposomeSet
tef | Function to get the Threshold for effective tests (TEF)
tef-method | Class ExWAS
toES | Method to convert an imExposomeSet to an ExposomeSet
toES-method | Class imExposomeSet
trans | Function to apply a transformation to the exposures of an ExposomeSet
trans-method | Class ExposomeSet

## -- V --

volcano_plot | Function to draw a Volcano Plot

## -- misc --

[ | Class imExposomeSet
[-method | Class imExposomeSet
[[-method | Class imExposomeSet