# omicRexposome
## Summary
`omicRexposome` is an R package for extending `rexposome` capabilities and inclide exposome-omic data analysis and integration. It depends in a series of third party R packages to provide:
1. [UNDER DEVELOPMENT] A series of pipelines to test exposome-omic and diseasome-omic associations.
* Basic GWAS pipeline based on `snpStats`
* Gene Expression Association Analysis based on `limma`
* Methylation Levels Association Analysis based on `MEAL`
* Proteine Level Association Analysis based on `limma`
2. [UNDER DEVELOPMENT] Two different approaches to integrate exposome with omic data.
## Installation
`omicRexposome` requires R version equal or newer than 3.3.0. The following script allows to install `rexposome` dependencies:
```r
source( "http://bioconductor.org/biocLite.R" )
packages = c('Biobase', 'MultiDataSet', 'BiocInstaller', 'gridExtra', 'stringr',
'ggplot2', 'reshape2', 'snpStats', 'MEAL', 'limma', 'sva', 'glmnet',
'omicade4', 'ggrepel', 'PMA', 'qqman'
)
for( pkg in packages ) {
if( !pkg %in% rownames( installed.packages() ) ) {
message( "Installing ", pkg )
biocLite( 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 basi dependence `rexposome`:
```r
devtools::install_github("isglobal-brge/rexposome")
devtools::install_github("isglobal-brge/omicRexposome")
```
### Details
## Basic Guide
### Loading Exposome
### Loading Omics
### Exposome-Omic Association
* Function `assocSNP` allows to perform a basic GWAS.
* Function `assocGE` allows to perform a DE analysis in base of the exposures.
* Function `assocME` allows to perform an EWAS for each exposure.
* Function `assocPRT` allows to test the association of the protein quantification with the exposures levels.
* `plotAssociation` allows to plot the result of all _assoc*_ functions.
### Exposome-Omic Integration
* Function `crossomics` allows to perform a multi-omic integration join exposome by selecting one of the available methods (`"mcia"` or `"mcca"`).
* `plotIntegration` allows to plot the results of `crossomics`.
