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:
- 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 onlimma
- Two different approaches to integrate exposome with omic data are implemented using multiple co-inertia analysis from
omicade4
and multi canonical correlation analysis fromPMA
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")
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 argumenttype
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 argumentstPV
(significant P-Value) andtFC
(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 ofcrossomics
, having a proper visualization for each method.