Package: rexposome 1.33.0

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]

rexposome_1.33.0.tar.gz
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rexposome_1.33.0.tar.gz(r-4.6-any)rexposome_1.33.0.tar.gz(r-4.5-any)
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rexposome.pdf |rexposome.html✨
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-1.33.0(bioc 3.23)rexposome-1.32.0(bioc 3.22)

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

software biologicalquestion infrastructure dataimport datarepresentation biomedicalinformatics experimentaldesign multiplecomparison classification clustering

5.72 score 1 packages 29 scripts 408 downloads 3 mentions 43 exports 169 dependencies

Last updated from:089d8b128c. Checks:1 FAILURE, 7 FAIL, 1 OK, 1 WARNING. Indexed: yes.

The latest version of this package failed to build. Look at thebuild logs for more information.

Target	Result	Time
bioc-checks	FAILURE	208
linux-devel-x86_64	FAIL	222
source / vignettes	OK	311
linux-release-x86_64	WARNING	290
macos-devel-arm64	FAIL	97
macos-release-arm64	FAIL	79
windows-devel	FAIL	72
windows-release	FAIL	80
windows-oldrel	FAIL	83
wasm-release	FAIL	160

Exports:classification clustering correlation expos exposureNames extract exwas familyNames get_robust_sd highAndLow ilod imputation imputeLOD invExWAS loadExposome loadExposome_plain loadImputed mexwas ndim normalityTest pca phenotypeNames plot3PCA plotClassification plotCorrelation plotEffect plotEXP plotExwas plotFamily plotHistogram plotLOD plotMissings plotPCA plotPHE plotVolcano readExposome standardize tableLOD tableMissings tef toES trans volcano_plot

Dependencies:abind backports base64enc Biobase BiocGenerics bit bit64 bitops boot broom bslib cachem car carData caTools checkmate circlize cli clipr cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table Deriv digest doBy dplyr DT ellipse emmeans estimability evaluate FactoMineR farver fastmap flashClust fontawesome forcats foreach forecast foreign Formula fracdiff fs generics ggplot2 ggrepel ggridges glmnet GlobalOptions glue gmm gplots gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets impute imputeLCMD isoband iterators jomo jquerylib jsonlite KernSmooth knitr labeling later lattice lazyeval leaps lifecycle lme4 lmtest lobstr lsr magrittr MASS Matrix MatrixModels memoise mgcv mice microbenchmark mime minqa mitml modelr multcompView mvtnorm nlme nloptr nnet norm numDeriv ordinal otel pan pbkrtest pcaMethods pillar pkgconfig plyr prettyunits progress promises pryr purrr quadprog quantmod quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readr reformulas reshape2 rlang rmarkdown rpart rstudioapi S4Vectors S7 sandwich sass scales scatterplot3d shape SparseM stringi stringr survival tibble tidyr tidyselect timeDate tinytex tmvtnorm tseries TTR tzdb ucminf urca utf8 vctrs viridisLite vroom withr xfun xts yaml zoo

Dealing with Multiple Imputations

Carles Hernandez-Ferrer and Juan R. Gonzalez

Rendered frommutiple_imputation_data_analysis.Rmdusingknitr::rmarkdownon Feb 15 2026.

Last update: 2024-02-07
Started: 2017-03-10

Exposome Data Analysis

Carles Hernandez-Ferrer, Xavier Escriba-Montagut, Juan R. Gonzalez

Rendered fromexposome_data_analysis.Rmdusingknitr::rmarkdownon Feb 15 2026.

Last update: 2024-02-07
Started: 2017-03-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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