Nothing
## ----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'-------------------------
# # For now
# devtools::install_github("bhklab/ToxicoGx", build_manual=TRUE,
# build_vignettes=TRUE)
#
# # Once accepted, submission in progress
# BiocManager::install("ToxicoGx")
## ---- message = FALSE, fig.width = 8, fig.height = 3--------------------------
library(PharmacoGx)
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(PharmacoGx::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')
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