## ----setup, include = FALSE, cache = FALSE, message = FALSE------------------- library("knitr") ### Chunk options: see http://yihui.name/knitr/options/ ### ## Text results opts_chunk$set(echo = TRUE, warning = TRUE, message = FALSE, include = TRUE) ## Cache opts_chunk$set(cache = 3, cache.path = "output/cache/") ## Plots opts_chunk$set(fig.path = "output/figures/") ## ----eval = FALSE, message = FALSE, results = 'hide'-------------------------- # BiocManager::install("ToxicoGx") ## ----message = FALSE, fig.width = 8, fig.height = 3--------------------------- library(CoreGx) library(ToxicoGx) library(ggplot2) # Load the tset data(TGGATESsmall) ToxicoGx::drugGeneResponseCurve(TGGATESsmall, duration = c("2", "8", "24"), cell_lines = "Hepatocyte", mDataTypes = "rna", features = "ENSG00000140465_at", dose = c("Control", "Low", "Middle", "High"), drug = "Carbon tetrachloride", ggplot_args = list(labs(title="Effect of Carbon tetra chloride on CYP1A1")), summarize_replicates = FALSE ) ## ----echo = FALSE, out.width="500px"------------------------------------------ knitr::include_graphics('CS1_published.png') ## ----results = 'asis', warnings=FALSE----------------------------------------- library(xtable) data("TGGATESsmall") # To compute the effect of drug concentration on the molecular profile of the cell drug.perturbation <- ToxicoGx::drugPerturbationSig(tSet = TGGATESsmall, mDataType = "rna", cell_lines = "Hepatocyte", duration = "24", features = fNames(TGGATESsmall, "rna"), dose = c("Control", "Low"), drugs = c("Omeprazole", "Isoniazid"), returnValues=c("estimate","tstat", "pvalue", "fdr"), verbose = FALSE) data(HCC_sig) res <- apply(drug.perturbation[,,c("tstat", "fdr")], 2, function(x, HCC){ return(CoreGx::connectivityScore(x = x, y = HCC[, 2, drop = FALSE], method = "fgsea", nperm=100)) }, HCC = HCC_sig[seq_len(195),]) rownames(res) <- c("Connectivity", "P Value") res <- t(res) res <- cbind(res,"FDR" = p.adjust(res[,2], method = "fdr")) res <- res[order(res[,3]),] knitr::kable(res, caption = 'Connectivity Score results for HCC and TG-GATEs PHH gene signature')