| Method to get the classification of the samples from an ExposomeClust. | classification |
| Method to perform clustering on the samples of an ExposomeSet | clustering |
| Creation of an ExposomeCorr from an ExposomeSet. | correlation |
| 'imExposomeSet' for testing purpouses | ex_imp |
| 'ExposomeSet' for testing purpouses | expo |
| 'ExposomeClust' for testing purpouses | expo_c |
| Returns the exposures matrix of an ExposomeSet. | expos |
| Class ExposomeClust | classification,ExposomeClust-method ExposomeClust ExposomeClust-class plot,ExposomeClust,ANY-method plotClassification,ExposomeClust-method sampleNames,ExposomeClust-method |
| Class ExposomeCorr | dim,ExposomeCorr-method ExposomeCorr ExposomeCorr-class extract,ExposomeCorr-method plot,ExposomeCorr,ANY-method plotCorrelation,ExposomeCorr-method |
| Class ExposomePCA | ExposomePCA ExposomePCA-class exposureNames,ExposomePCA-method extract,ExposomePCA-method ndim,ExposomePCA-method phenotypeNames,ExposomePCA-method plot,ExposomePCA,ANY-method plot3PCA,ExposomePCA-method plotEXP,ExposomePCA-method plotPCA,ExposomePCA-method plotPHE,ExposomePCA-method |
| Class ExposomeSet | clustering,ExposomeSet-method correlation,ExposomeSet-method dim,ExposomeSet-method expos,ExposomeSet-method ExposomeSet ExposomeSet-class exposureNames,ExposomeSet-method exwas,ExposomeSet-method familyNames,ExposomeSet-method highAndLow,ExposomeSet-method ilod,ExposomeSet-method imputation,ExposomeSet-method invExWAS,ExposomeSet-method mexwas,ExposomeSet-method normalityTest,ExposomeSet-method pca,ExposomeSet-method phenotypeNames,ExposomeSet-method plot,ExposomeSet,ANY-method plotFamily,ExposomeSet-method plotHistogram,ExposomeSet-method plotLOD,ExposomeSet-method plotMissings,ExposomeSet-method standardize,ExposomeSet-method Summary,ExposomeSet-method tableLOD,ExposomeSet-method tableMissings,ExposomeSet-method trans,ExposomeSet-method |
| Getter to obtain the exposures's names of an ExposomeSet or ExposomePCA | exposureNames |
| Raw data from 'ExWAS', 'ExposomeClust' and 'ExposomeCorr'. | extract |
| Testing the association between an exposure and a phenotype of an ExposomeSet | exwas |
| Class ExWAS | extract,ExWAS-method ExWAS ExWAS-class get_robust_sd,ExWAS-method names,ExWAS-method plot,ExWAS,ANY-method plotEffect,ExWAS-method plotExwas,ExWAS-method plotVolcano,ExWAS-method tef,ExWAS-method |
| Getter to obtain the exposures's names of an ExposomeSet. | familyNames |
| Raw data from 'ExWAS' | extract get_robust_sd |
| Function to convert continuous exposures to categorical exposures | highAndLow |
| Function to impute under-LOD values from an ExposomeSet | ilod |
| Class imExposomeSet | dim,imExposomeSet-method expos,imExposomeSet-method exposureNames,imExposomeSet-method extract,imExposomeSet-method exwas,imExposomeSet-method familyNames,imExposomeSet-method imExposomeSet imExposomeSet-class imExposomeSet-methods phenotypeNames,imExposomeSet-method plot,imExposomeSet,ANY-method plotFamily,imExposomeSet-method sampleNames,imExposomeSet-method toES,imExposomeSet-method [ [,imExposomeSet,ANY,ANY,ANY-method [[,imExposomeSet-method |
| Function to impute missing values from an ExposomeSet | imputation |
| Function to impute values under limit of detection | imputeLOD |
| Testing the association between an exposure and a phenotype of an ExposomeSet (modelling the exposures as response) | invExWAS |
| Creation of an ExposomeSet from 'data.frames' | loadExposome |
| Creation of an ExposomeSet from single 'data.frame' | loadExposome_plain |
| Creation of an imExposomeSet from 'data.frames' | loadImputed |
| 'data.frame' for testing purpouses | me |
| Testing the association between an exposure and a phenotype of an ExposomeSet using a multivariate aproach. | mexwas |
| Class mExWAS | extract,mExWAS-method mExWAS mExWAS-class plot,mExWAS,ANY-method plotExwas,mExWAS-method |
| Number of principal components in an ExposomePCA. | ndim |
| It creates a 'data.frame' of boolean indicating if the exposures follows a normal distribution or not. | normalityTest |
| Creation of an ExposomePCA from an ExposomeSet. | pca |
| Getter to obtain the phenotype's names of an ExposomeSet or ExposomePCA. | phenotypeNames |
| Ploting PCA in a 3D space | plot3PCA |
| Draw the profile of the levels exposures after a classification with a clustering method | plotClassification |
| It draws both circos or matrix plot for the correlation in ExposomeCorr | plotCorrelation |
| Function to draw a plot of the pvalues stored in an 'ExWAS' object | plotEffect |
| Plot correlation between exposures and PCA | plotEXP |
| Function to draw a plot of the pvalues stored in an 'ExWAS' object | plotExwas |
| It draws the profile of the exposome in an ExposomeSet | plotFamily |
| It draws a histogram for each exposure in an ExposomeSet | plotHistogram |
| It draws a chart with the percentage of under-LOD values in an ExposomeSet | plotLOD |
| It draws a chart with the percentage of missing in an ExposomeSet | plotMissings |
| Ploting PCA | plotPCA |
| Plot association score between phentoypes and PCA | plotPHE |
| Function to draw a plot of the pvalues stored in an 'ExWAS' object | plotVolcano |
| Creation of an ExposomeSet from files | readExposome |
| rexposome: Package for exposome exploration and outcome data analysis | rexposome |
| #' 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 |
| It creates a vector with the amount of under-LOD exposures in an ExposomeSet | tableLOD |
| It creates a vector with the amount of missing in an ExposomeSet | tableMissings |
| Function to get the Threshold for effective tests (TEF) | tef |
| Method to convert an imExposomeSet to an ExposomeSet | toES |
| Function to apply a transformation to the exposures of an ExposomeSet | trans |
| Function to draw a Volcano Plot | volcano_plot |
