rexposome is an R package for exposome characterization and exopsome-outcome test association. It depends in a series of third party R packages to provide:

  1. A basic pipeline for missing-data imputation in exposome, include the imputation of values under limit of detection.
  2. A series of functions to describe and characterize the exposome, including PCA in exposures and samples space, correlation between exposures and clustering of samples through exposure levels.
  3. Two different approaches to test the association exposome-diseasom in terms of Exposome-Wide Association Studies (ExWAS and mExWAS).


rexposome requires R version equal or newer than 3.0. The following script allows to install rexposome dependencies:

if (!requireNamespace("BiocManager", quietly=TRUE))

packages = c('Biobase', 'mice', 'MultiDataSet', 'lsr', 'FactoMineR',
    'stringr', 'circlize', 'corrplot', 'ggplot2', 'reshape2', 'pryr',
    'scales', 'imputeLCMD', 'scatterplot3d', 'glmnet', 'gridExtra',
    'grid', 'Hmisc', 'gplots', 'gtools', 'S4Vectors'
for( pkg in packages ) {
  if( !pkg %in% rownames( installed.packages() ) ) {
    message( "Installing ", pkg )
    BiocManager::install( pkg )

The package can be installed using the R package devtools. devtools can be installed win the following code:


Due to the publication process of rexposome at Biocondcuto, the requirment is set to R-3.4. For those using R-3.4, the following code installs rexposome:


For those using an older version of R (but newer than R-3.o) the following code installs rexposome:

devtools::install_github("isglobal-brge/rexposome", ref="R-3.0")



Loading Exposome

In rexposome the exposome is understood as a set of three files:

  1. The exposure file: A matrix files with the exposures' measurements, having the individuals as rows and the exposures as columns.
  2. The phenotype file (diseasome file): A matrix with the phenotypes or diseases description, having the individuals as rows and the phenotypes as columns.
  3. The description file: A table describing the exposures. It must have, at last, two columns: one with the exposures and one with the family/group of exposures. The order of the exposures must be the same as in exposure-file.

The exposome is loaded from files using the function readExposome. If the information is stored in standard R data.frames, those can be converted to an ExposomeSet using the function loadExposome.

Exposome Characterization

The characterization of the exposome is done with a bunch of functions that follows:

Exposome-Phenotype Association

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rexposome documentation built on March 13, 2021, 2:01 a.m.