{ "_id": "6a103acfacfb0bcc41c9b4a7", "Package": "rexposome", "Version": "1.35.0", "Title": "Exposome exploration and outcome data analysis", "Authors@R": "c(person(\"Carles\", \"Hernandez-Ferrer\", , \"carles.hernandez@isglobal.org\", c(\"aut\", \"cre\")),\nperson(\"Juan R.\", \"Gonzalez\", ,\"juanr.gonzalez@isglobal.org\", role = \"aut\"),\nperson(\"Xavier\", \"Escribà-Montagut\", ,\"xavier.escriba@isglobal.org\", role = \"aut\"))", "Maintainer": "Xavier Escribà Montagut ", "Description": "Package that allows to explore the exposome and to perform\nassociation analyses between exposures and health outcomes.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.2.1", "VignetteBuilder": "knitr", "biocViews": "Software, BiologicalQuestion, Infrastructure, DataImport,\nDataRepresentation, BiomedicalInformatics, ExperimentalDesign,\nMultipleComparison, Classification, Clustering", "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev libx11-dev\nzlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-05-11 17:35:33 UTC", "RemoteUrl": "https://github.com/bioc/rexposome", "RemoteRef": "HEAD", "RemoteSha": "2a65b5f87612f67d196aae2a521620654e05ab0a", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-11 22:09:20 UTC", "User": "root" }, "Author": "Carles Hernandez-Ferrer [aut, cre],\nJuan R. Gonzalez [aut],\nXavier Escribà-Montagut [aut]", "MD5sum": "57a2ae6b17c9e070b1c47fc1225f62d7", "_user": "bioc", "_type": "src", "_file": "rexposome_1.35.0.tar.gz", "_fileid": "675eaae0fc1c357d4bdc14c43447ccddc73685a5e7825897ae6acb7faef2328b", "_filesize": 8260619, "_sha256": "675eaae0fc1c357d4bdc14c43447ccddc73685a5e7825897ae6acb7faef2328b", "_created": "2026-05-11T22:09:20.000Z", "_published": "2026-05-22T11:15:27.320Z", "_distro": "noble", "_jobs": [ { "job": 77368477054, "time": 213, "config": "bioc-checks", "r": "4.6.0", "check": "FAILURE", "artifact": "" }, { "job": 77368476831, "time": 380, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "6931145849" }, { "job": 77368477148, "time": 328, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "6931131894" }, { "job": 77368476976, "time": 209, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "6931098382" }, { "job": 77368476713, "time": 169, 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"eclust", "class": [ "ExposomeClust" ], "fields": [], "table": false, "tojson": false }, { "name": "me", "title": "'data.frame' for testing purpouses", "object": "me", "class": [ "data.frame" ], "fields": [ ".imp", ".id", "DDE", "DDT", "HCB", "bHCH", "PCB118", "PCB153", "PCB180", "PCB138", "BPA", "THM", "CHCl3", "BTHM", "Cotinine", "Gas", "ETS", "H_pesticides", "G_pesticides", "Benzene", "PM25CU", "PM25FE", "PM25K", "PM25Ni", "PM25S", "PM25Sl", "PM25V", "PM25Zn", "PM10Cu", "PM10Fe", "PM10K", "PM10Ni", "PM10S", "PM10SI", "PM10V", "PM10Zn", "NO2", "NO", "NOx", "PM25", "PM10", "PMcoarse", "AbsPM25", "Dens", "Conn", "Green", "Noise_d", "Noise_n", "Temp", "whistling_chest", "flu", "rhinitis", "wheezing", "sex", "age", "cbmi", "blood_pre" ], "rows": 654, "table": true, "tojson": true } ], "_help": [ { "page": "classification-methods", "title": "Method to get the classification of the samples from an ExposomeClust.", "topics": [ "classification" ] }, { "page": "clustering-methods", "title": "Method to perform clustering on the samples of an ExposomeSet", "topics": [ "clustering" ] }, { "page": "correlation-methods", "title": "Creation of an ExposomeCorr from an ExposomeSet.", "topics": [ "correlation" ] }, { "page": "ex_imp", "title": "'imExposomeSet' for testing purpouses", "topics": [ "ex_imp" ] }, { "page": "expo", "title": "'ExposomeSet' for testing purpouses", "topics": [ "expo" ] }, { "page": "expo_c", "title": "'ExposomeClust' for testing purpouses", "topics": [ "expo_c" ] }, { "page": "expos-methods", "title": "Returns the exposures matrix of an ExposomeSet.", "topics": [ "expos" ] }, { "page": "ExposomeClust-class", "title": "Class ExposomeClust", "topics": [ "classification,ExposomeClust-method", "ExposomeClust", "ExposomeClust-class", "plot,ExposomeClust,ANY-method", "plotClassification,ExposomeClust-method", "sampleNames,ExposomeClust-method" ] }, { "page": "ExposomeCorr-class", "title": "Class ExposomeCorr", "topics": [ "dim,ExposomeCorr-method", "ExposomeCorr", "ExposomeCorr-class", "extract,ExposomeCorr-method", "plot,ExposomeCorr,ANY-method", "plotCorrelation,ExposomeCorr-method" ] }, { "page": "ExposomePCA-class", "title": "Class ExposomePCA", "topics": [ "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" ] }, { "page": "ExposomeSet-class", "title": "Class ExposomeSet", "topics": [ "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" ] }, { "page": "exposureNames-methods", "title": "Getter to obtain the exposures's names of an ExposomeSet or ExposomePCA", "topics": [ "exposureNames" ] }, { "page": "extract-methods", "title": "Raw data from 'ExWAS', 'ExposomeClust' and 'ExposomeCorr'.", "topics": [ "extract" ] }, { "page": "exwas-methods", "title": "Testing the association between an exposure and a phenotype of an ExposomeSet", "topics": [ "exwas" ] }, { "page": "ExWAS-class", "title": "Class ExWAS", "topics": [ "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" ] }, { "page": "familyNames-methods", "title": "Getter to obtain the exposures's names of an ExposomeSet.", "topics": [ "familyNames" ] }, { "page": "get_robust_sd-methods", "title": "Raw data from 'ExWAS'", "topics": [ "extract", "get_robust_sd" ] }, { "page": "highAndLow-methods", "title": "Function to convert continuous exposures to categorical exposures", "topics": [ "highAndLow" ] }, { "page": "ilod-methods", "title": "Function to impute under-LOD values from an ExposomeSet", "topics": [ "ilod" ] }, { "page": "imExposomeSet-class", "title": "Class imExposomeSet", "topics": [ "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" ] }, { "page": "imputation-methods", "title": "Function to impute missing values from an ExposomeSet", "topics": [ "imputation" ] }, { "page": "imputeLOD", "title": "Function to impute values under limit of detection", "topics": [ "imputeLOD" ] }, { "page": "invExWAS-methods", "title": "Testing the association between an exposure and a phenotype of an ExposomeSet (modelling the exposures as response)", "topics": [ "invExWAS" ] }, { "page": "loadExposome", "title": "Creation of an ExposomeSet from 'data.frames'", "topics": [ "loadExposome" ] }, { "page": "loadExposome_plain", "title": "Creation of an ExposomeSet from single 'data.frame'", "topics": [ "loadExposome_plain" ] }, { "page": "loadImputed", "title": "Creation of an imExposomeSet from 'data.frames'", "topics": [ "loadImputed" ] }, { "page": "me", "title": "'data.frame' for testing purpouses", "topics": [ "me" ] }, { "page": "mexwas-methods", "title": "Testing the association between an exposure and a phenotype of an ExposomeSet using a multivariate aproach.", "topics": [ "mexwas" ] }, { "page": "mExWAS-class", "title": "Class mExWAS", "topics": [ "extract,mExWAS-method", "mExWAS", "mExWAS-class", "plot,mExWAS,ANY-method", "plotExwas,mExWAS-method" ] }, { "page": "ndim-methods", "title": "Number of principal components in an ExposomePCA.", "topics": [ "ndim" ] }, { "page": "normalityTest-methods", "title": "It creates a 'data.frame' of boolean indicating if the exposures follows a normal distribution or not.", "topics": [ "normalityTest" ] }, { "page": "pca-methods", "title": "Creation of an ExposomePCA from an ExposomeSet.", "topics": [ "pca" ] }, { "page": "phenotypeNames-methods", "title": "Getter to obtain the phenotype's names of an ExposomeSet or ExposomePCA.", "topics": [ "phenotypeNames" ] }, { "page": "plot3PCA-methods", "title": "Ploting PCA in a 3D space", "topics": [ "plot3PCA" ] }, { "page": "plotClassification-methods", "title": "Draw the profile of the levels exposures after a classification with a clustering method", "topics": [ "plotClassification" ] }, { "page": "plotCorrelation-methods", "title": "It draws both circos or matrix plot for the correlation in ExposomeCorr", "topics": [ "plotCorrelation" ] }, { "page": "plotEffect-methods", "title": "Function to draw a plot of the pvalues stored in an 'ExWAS' object", "topics": [ "plotEffect" ] }, { "page": "plotEXP-methods", "title": "Plot correlation between exposures and PCA", "topics": [ "plotEXP" ] }, { "page": "plotExwas-methods", "title": "Function to draw a plot of the pvalues stored in an 'ExWAS' object", "topics": [ "plotExwas" ] }, { "page": "plotFamily-methods", "title": "It draws the profile of the exposome in an ExposomeSet", "topics": [ "plotFamily" ] }, { "page": "plotHistogram-methods", "title": "It draws a histogram for each exposure in an ExposomeSet", "topics": [ "plotHistogram" ] }, { "page": "plotLOD-methods", "title": "It draws a chart with the percentage of under-LOD values in an ExposomeSet", "topics": [ "plotLOD" ] }, { "page": "plotMissings-methods", "title": "It draws a chart with the percentage of missing in an ExposomeSet", "topics": [ "plotMissings" ] }, { "page": "plotPCA-methods", "title": "Ploting PCA", "topics": [ "plotPCA" ] }, { "page": "plotPHE-methods", "title": "Plot association score between phentoypes and PCA", "topics": [ "plotPHE" ] }, { "page": "plotVolcano-methods", "title": "Function to draw a plot of the pvalues stored in an 'ExWAS' object", "topics": [ "plotVolcano" ] }, { "page": "readExposome", "title": "Creation of an ExposomeSet from files", "topics": [ "readExposome" ] }, { "page": "rexposome", "title": "rexposome: Package for exposome exploration and outcome data analysis", "topics": [ "rexposome" ] }, { "page": "standardize-methods", "title": "#' 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.", "topics": [ "standardize" ] }, { "page": "tableLOD-methods", "title": "It creates a vector with the amount of under-LOD exposures in an ExposomeSet", "topics": [ "tableLOD" ] }, { "page": "tableMissings-methods", "title": "It creates a vector with the amount of missing in an ExposomeSet", "topics": [ "tableMissings" ] }, { "page": "tef-methods", "title": "Function to get the Threshold for effective tests (TEF)", "topics": [ "tef" ] }, { "page": "toES", "title": "Method to convert an imExposomeSet to an ExposomeSet", "topics": [ "toES" ] }, { "page": "trans-methods", "title": "Function to apply a transformation to the exposures of an ExposomeSet", "topics": [ "trans" ] }, { "page": "volcano_plot", "title": "Function to draw a Volcano Plot", "topics": [ "volcano_plot" ] } ], "_readme": "https://github.com/bioc/rexposome/raw/HEAD/README.md", "_rundeps": [ "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", "data.table", "Deriv", "digest", "doBy", "dplyr", "DT", "ellipse", "emmeans", 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