Name Mode Size
exposome_omic_integration.Rmd 100644 14 kb
# 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: ```r 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: ```r install.packages("devtools") ``` Once `devtools` and the dependences are installed, the following code installs `omicRexposome` and the basic dependence `rexposome`: ```r 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 `ExpressionSet`s (plus `ExposomeSet`s). * `plotIntegration` allows to plot the results of `crossomics`, having a proper visualization for each method.