## ----setup, include=FALSE----------------------------------------------------- BiocStyle::markdown() knitr::opts_chunk$set(echo = TRUE, warnings=FALSE, crop = NULL) ## ----eval=FALSE--------------------------------------------------------------- # devtools::install_github("isglobal-brge/omicRexposome") ## ----load_omicRexposome, message=FALSE---------------------------------------- library(omicRexposome) library(MultiDataSet) ## ----expos_data, cache=FALSE-------------------------------------------------- data("brge_expo", package = "brgedata") class(brge_expo) ## ----gexp_data, cache=FALSE--------------------------------------------------- data("brge_gexp", package = "brgedata") ## ----gexp_analysis, message=FALSE, warning=FALSE------------------------------ mds <- createMultiDataSet() mds <- add_genexp(mds, brge_gexp) mds <- add_exp(mds, brge_expo) gexp <- association(mds, formula=~Sex+Age, expset = "exposures", omicset = "expression") ## ----gexp_tables-------------------------------------------------------------- hit <- tableHits(gexp, th=0.001) lab <- tableLambda(gexp) merge(hit, lab, by="exposure") ## ----gexp_analysis_sva, message=FALSE, warning=FALSE-------------------------- gexp <- association(mds, formula=~Sex+Age, expset = "exposures", omicset = "expression", sva = "fast") ## ----gexp_tables_sva---------------------------------------------------------- hit <- tableHits(gexp, th=0.001) lab <- tableLambda(gexp) merge(hit, lab, by="exposure") ## ----gexp_plot_qq------------------------------------------------------------- gridExtra::grid.arrange( plotAssociation(gexp, rid="Ben_p", type="qq") + ggplot2::ggtitle("Transcriptome - Pb Association"), plotAssociation(gexp, rid="BPA_p", type="qq") + ggplot2::ggtitle("Transcriptome - THM Association"), ncol=2 ) ## ----gexp_plot_volcano-------------------------------------------------------- gridExtra::grid.arrange( plotAssociation(gexp, rid="Ben_p", type="volcano", tPV=-log10(1e-04)) + ggplot2::ggtitle("Transcriptome - Pb Association"), plotAssociation(gexp, rid="BPA_p", type="volcano", tPV=-log10(1e-04)) + ggplot2::ggtitle("Transcriptome - THM Association"), ncol=2 ) ## ----prot_data, cache=FALSE--------------------------------------------------- data("brge_prot", package="brgedata") brge_prot ## ----prot_analysis, message=FALSE, warning=FALSE------------------------------ mds <- createMultiDataSet() mds <- add_eset(mds, brge_prot, dataset.type ="proteome") mds <- add_exp(mds, brge_expo) prot <- association(mds, formula=~Sex+Age, expset = "exposures", omicset = "proteome") ## ----prot_hits---------------------------------------------------------------- tableHits(prot, th=0.001) ## ----prot_plot_volcano-------------------------------------------------------- gridExtra::grid.arrange( plotAssociation(prot, rid="Ben_p", type="protein") + ggplot2::ggtitle("Proteome - Cd Association") + ggplot2::geom_hline(yintercept = 1, color = "LightPink"), plotAssociation(prot, rid="NO2_p", type="protein") + ggplot2::ggtitle("Proteome - Cotinine Association") + ggplot2::geom_hline(yintercept = 1, color = "LightPink"), ncol=2 ) ## ----rm_asc, echo=FALSE, message=FALSE---------------------------------------- rm(prot, gexp) gc() ## ----missing_exp, message=FALSE----------------------------------------------- library(rexposome) plotMissings(brge_expo, set = "exposures") ## ----impute_exp, message=FALSE------------------------------------------------ brge_expo <- imputation(brge_expo) ## ----crossomics_mcia, message=FALSE, warning=FALSE---------------------------- mds <- createMultiDataSet() mds <- add_genexp(mds, brge_gexp) mds <- add_eset(mds, brge_prot, dataset.type = "proteome") mds <- add_exp(mds, brge_expo) cr_mcia <- crossomics(mds, method = "mcia", verbose = TRUE) cr_mcia ## ----crossomics_mcca, message=FALSE, warning=FALSE, results='hide'------------ cr_mcca <- crossomics(mds, method = "mcca", permute=c(4, 2)) cr_mcca ## ----integration_colors------------------------------------------------------- colors <- c("green", "blue", "red") names(colors) <- names(mds) ## ----plot_pe_mcia, messages=FALSE, warnings=FALSE----------------------------- plotIntegration(cr_mcia, colors=colors) ## ----plot_pe_mcca, messages=FALSE, warnings=FALSE, fig.height=8, fig.width=9---- plotIntegration(cr_mcca, colors=colors) ## ----rm_crs------------------------------------------------------------------- rm(cr_mcia, cr_mcca) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()