Exposome exploration and outcome data analysis

Documentation for package ‘rexposome’ version 1.31.0

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-- 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