Package: rexposome 1.35.0

Xavier Escribà Montagut

rexposome: Exposome exploration and outcome data analysis

Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.

Authors:Carles Hernandez-Ferrer [aut, cre], Juan R. Gonzalez [aut], Xavier Escribà-Montagut [aut]

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
rexposome/json (API)

# Install 'rexposome' in R:
install.packages('rexposome', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • ex_imp - 'imExposomeSet' for testing purpouses
  • expo - 'ExposomeSet' for testing purpouses
  • expo_c - 'ExposomeClust' for testing purpouses
  • me - 'data.frame' for testing purpouses

On BioConductor:rexposome-1.35.0(bioc 3.24)rexposome-1.34.2(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarebiologicalquestioninfrastructuredataimportdatarepresentationbiomedicalinformaticsexperimentaldesignmultiplecomparisonclassificationclustering

6.12 score 1 packages 29 scripts 484 downloads 3 mentions 43 exports 161 dependencies

Last updated from:2a65b5f876. Checks:1 FAILURE, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksFAILURE200
linux-devel-x86_64WARNING343
source / vignettesOK320
linux-release-x86_64WARNING288
macos-release-arm64WARNING166
macos-oldrel-arm64WARNING214
windows-develWARNING223
windows-releaseWARNING210
windows-oldrelWARNING196
wasm-releaseOK178

Exports:classificationclusteringcorrelationexposexposureNamesextractexwasfamilyNamesget_robust_sdhighAndLowilodimputationimputeLODinvExWASloadExposomeloadExposome_plainloadImputedmexwasndimnormalityTestpcaphenotypeNamesplot3PCAplotClassificationplotCorrelationplotEffectplotEXPplotExwasplotFamilyplotHistogramplotLODplotMissingsplotPCAplotPHEplotVolcanoreadExposomestandardizetableLODtableMissingsteftoEStransvolcano_plot

Dependencies:abindbackportsbase64encBiobaseBiocGenericsbitbit64bitopsbootbroombslibcachemcarcarDatacaToolscheckmatecirclizeclicliprclustercodetoolscolorspacecorrplotcowplotcpp11crayoncrosstalkdata.tableDerivdigestdoBydplyrDTellipseemmeansestimabilityevaluateFactoMineRfarverfastmapflashClustfontawesomeforcatsforeachforecastforeignFormulafracdifffsgenericsggplot2ggrepelggridgesglmnetGlobalOptionsgluegmmgplotsgridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetsimputeimputeLCMDisobanditeratorsjomojquerylibjsonliteKernSmoothknitrlabelinglaterlatticelazyevalleapslifecyclelme4lmtestlsrmagrittrMASSMatrixMatrixModelsmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmultcompViewmvtnormnlmenloptrnnetnormnumDerivordinalotelpanpbkrtestpcaMethodspillarpkgconfigplyrprettyunitsprogresspromisespurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRdpackreadrreformulasreshape2rlangrmarkdownrpartrstudioapiS4VectorsS7sandwichsassscalesscatterplot3dshapeSparseMstringistringrsurvivaltibbletidyrtidyselecttimeDatetinytextmvtnormtzdbucminfurcautf8vctrsviridisLitevroomwithrxfunyamlzoo

Dealing with Multiple Imputations
Introduction | Dummy Imputation with mice | Data Format | Creating an imExposomeSet | Accessing to Exposome Data | Exposures Behaviour | Extracting an ExposomeSet from an imExposomeSet | Exposome-Wide Association Studies (ExWAS) | Extract the exposures over the threshold of effective tests | Session info
Rendered frommutiple_imputation_data_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2017-03-10

Exposome Data Analysis
Introduction | Installation | Pipeline | Data Format | Three table format | Single table format | Analysis | Loading Exposome Data | From TXT files | From data.frame | Accessing to Exposome Data | Exposome Pre-process | Missing Data in Exposures and Phenotypes | Exposures Normality | Exposures Imputation | Exposures Characterization (i.e. data visualization) | Exposures PCA | Exposures Correlation | Individuals Clustering | Exposure associations | Understanding Principal Component Analysis | Exposure/Enviroment/Exposome Wide Association Studies (ExWAS) | Sensitivity analysis: stratified models | Inverse ExWAS | Variable selection ExWAS | Session info
Rendered fromexposome_data_analysis.Rmdusingknitr::rmarkdown

Last update: 2026-05-11
Started: 2017-03-06

Readme and manuals

Help Manual

Help pageTopics
Method to get the classification of the samples from an ExposomeClust.classification
Method to perform clustering on the samples of an ExposomeSetclustering
Creation of an ExposomeCorr from an ExposomeSet.correlation
'imExposomeSet' for testing purpousesex_imp
'ExposomeSet' for testing purpousesexpo
'ExposomeClust' for testing purpousesexpo_c
Returns the exposures matrix of an ExposomeSet.expos
Class ExposomeClustclassification,ExposomeClust-method ExposomeClust ExposomeClust-class plot,ExposomeClust,ANY-method plotClassification,ExposomeClust-method sampleNames,ExposomeClust-method
Class ExposomeCorrdim,ExposomeCorr-method ExposomeCorr ExposomeCorr-class extract,ExposomeCorr-method plot,ExposomeCorr,ANY-method plotCorrelation,ExposomeCorr-method
Class ExposomePCAExposomePCA 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 ExposomeSetclustering,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 ExposomePCAexposureNames
Raw data from 'ExWAS', 'ExposomeClust' and 'ExposomeCorr'.extract
Testing the association between an exposure and a phenotype of an ExposomeSetexwas
Class ExWASextract,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 exposureshighAndLow
Function to impute under-LOD values from an ExposomeSetilod
Class imExposomeSetdim,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 ExposomeSetimputation
Function to impute values under limit of detectionimputeLOD
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 purpousesme
Testing the association between an exposure and a phenotype of an ExposomeSet using a multivariate aproach.mexwas
Class mExWASextract,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 spaceplot3PCA
Draw the profile of the levels exposures after a classification with a clustering methodplotClassification
It draws both circos or matrix plot for the correlation in ExposomeCorrplotCorrelation
Function to draw a plot of the pvalues stored in an 'ExWAS' objectplotEffect
Plot correlation between exposures and PCAplotEXP
Function to draw a plot of the pvalues stored in an 'ExWAS' objectplotExwas
It draws the profile of the exposome in an ExposomeSetplotFamily
It draws a histogram for each exposure in an ExposomeSetplotHistogram
It draws a chart with the percentage of under-LOD values in an ExposomeSetplotLOD
It draws a chart with the percentage of missing in an ExposomeSetplotMissings
Ploting PCAplotPCA
Plot association score between phentoypes and PCAplotPHE
Function to draw a plot of the pvalues stored in an 'ExWAS' objectplotVolcano
Creation of an ExposomeSet from filesreadExposome
rexposome: Package for exposome exploration and outcome data analysisrexposome
#' 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 ExposomeSettableLOD
It creates a vector with the amount of missing in an ExposomeSettableMissings
Function to get the Threshold for effective tests (TEF)tef
Method to convert an imExposomeSet to an ExposomeSettoES
Function to apply a transformation to the exposures of an ExposomeSettrans
Function to draw a Volcano Plotvolcano_plot