omicRexposome

Summary

omicRexposome is an R package for extending rexposome capabilities and include exposome-omic data analysis and integration. It depends in a series of third party R packages to provide:

1. A series of pipelines to test exposome-omic and diseasome-omic associations. * [UNDER DEVELOPMENT] Basic GWAS pipeline based on snpStats * Methylome, Transcriptome and Proteome Association Analysis based on limma
2. Two different approaches to integrate exposome with omic data are implemented using multiple co-inertia analysis from omicade4 and multi canonical correlation analysis from PMA

Installation

omicRexposome requires R version equal or newer than 3.3.0. The following script allows to install rexposome dependencies:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")

packages = c('Biobase', 'methods', 'snpStats', 'limma', 'sva', 'ggplot2',
    'ggrepel', 'PMA', 'omicade4', 'ggplot2', 'qqman', 'gridExtra'
)
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:

install.packages("devtools")

Once devtools and the dependences are installed, the following code installs omicRexposome and the basic dependence rexposome:

devtools::install_github("isglobal-brge/rexposome")
devtools::install_github("isglobal-brge/omicRexposome")

Basic Guide

Exposome-Omic Association is done using the function assocES. This function requires an argument x being an ExposomeSet and an argument y being an ExpressionSet with the correct omic data (gene expression for transcriptome, betas or Ms for methylome, and protein level for proteome).

• plotAssociation allows to plot the result of all assoc* functions having an argument type that can takes:
  • "manhattan" to draw a typical Manhattan plot
  • "protein" to draw an adapted version of a Manhattan plot for protein data
  • "volcano" to draw a volcano plot, having the option to fill the arguments tPV (significant P-Value) and tFC (significant fold change)
  • "qq" to draw a standard QQ plot

Function crossomics allows to perform a multi-omic integration join exposome by selecting one of the available methods ("mcia" or "mcca"). The main argument, called list, must be filled with a list of ExpressionSets (plus ExposomeSets).

• plotIntegration allows to plot the results of crossomics, having a proper visualization for each method.