## ----setup, include = FALSE--------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----eval=FALSE--------------------------------------------------------------- # # install from bioconductor # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("pairkat") ## ----message=F, warning = F, results='hide'----------------------------------- # load pairkat library library(pairkat) data("smokers") ## ----message=F, warning = F--------------------------------------------------- phenotype <- SummarizedExperiment::colData(smokers) head(phenotype) ## ----------------------------------------------------------------------------- pathways <- SummarizedExperiment::rowData(smokers) head(pathways)[, 1:2] ## ----------------------------------------------------------------------------- metabolome <- SummarizedExperiment::assays(smokers)$metabolomics head(metabolome)[, 1:3] ## ----------------------------------------------------------------------------- smokers <- SummarizedExperiment::SummarizedExperiment( assays = list(metabolomics = metabolome), rowData = pathways, colData = phenotype ) ## ----------------------------------------------------------------------------- head(KEGGREST::keggList("organism"))[, 2:3] ## ----------------------------------------------------------------------------- networks <- GatherNetworks( SE = smokers, keggID = "kegg_id", species = "hsa", minPathwaySize = 5 ) ## ----message = F, warning = F------------------------------------------------- # run PaIRKAT output <- PaIRKAT(log_FEV1_FVC_ratio ~ age, networks = networks) ## ----------------------------------------------------------------------------- # view formula call output$call # view results results <- dplyr::arrange(output$results, p.value) head(results) ## ----------------------------------------------------------------------------- plotNetworks(networks = networks, pathway = "Glycerophospholipid metabolism") ## ----------------------------------------------------------------------------- sessionInfo()