# # - - - - -设置,包括= FALSE,缓存= FALSE,消息= FALSE - - - - - - - - - - - - - - - - - - -库(knitr) # # #块选项:参见http://yihui.name/knitr/options/ opts_chunk $ # # # # #文本结果集(呼应= TRUE,警告= TRUE,消息= FALSE,包括= TRUE) # #缓存opts_chunk美元集(缓存= 3,缓存。路径= "输出缓存/”)# #地块opts_chunk美元设置(图。路径= "输出/数据/”)# # - - - - - eval = FALSE,消息= FALSE,结果=“隐藏”- - - - - - - - - - - - - - - - - - - - - - - - -现在# # # devtools:: install_github (build_manual = TRUE, " bhklab / ToxicoGx " # build_vignettes = TRUE) # # #一旦接受,提交进展# BiocManager::安装(“ToxicoGx”) # #——消息= FALSE, fig.width = 8, fig.height = 3 - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(PharmacoGx)库(ToxicoGx)库(ggplot2) #加载tset数据(TGGATESsmall) ToxicoGx:: drugGeneResponseCurve (TGGATESsmall、持续时间= c (“2”,“8”,“24”), cell_lines =“肝细胞”,mDataTypes =“rna”特性=“ENSG00000140465_at剂量= c(“控制”、“低”、“中”,“高”),药物=“四氯化碳ggplot_args =列表(实验室(title =“碳四氯对CYP1A1的影响”)),summarize_replicates = FALSE) # #——回声= FALSE,。宽度= " 500 px”- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - knitr:: include_graphics (CS1_published.png) # #——结果=“黑名单”,警告= FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -库(xtable)数据(“TGGATESsmall”) #计算药物浓度的影响在分子细胞的药物。扰动< - ToxicoGx:: drugPerturbationSig (tSet = TGGATESsmall mDataType =“rna cell_lines =“肝细胞”=“24”,持续时间特性=帧(TGGATESsmall,“rna”),剂量= c(“控制”,“低”),药物= c(“奥美拉唑”,“异烟肼”),returnvalue = c(“估计”、“tstat”,“pvalue”、“罗斯福”),详细= FALSE)数据(HCC_sig) res < -应用(药物。扰动(,c (“tstat”、“罗斯福”)],2,函数(x, HCC){返回(PharmacoGx: connectivityScore (x = x, y =肝细胞癌(,2 = FALSE)下降,方法=“fgsea”, nperm = 100))}, HCC = HCC_sig [seq_len (195)]) rownames (res) < - c(“连接”、“P值”)res < - t (res) res < cbind (res,“罗斯福”= P。调整(res[2],方法=“罗斯福”))res < - res(顺序(res [3]),] knitr:: kable (res,标题=对HCC的连通性评分结果和收购PHH TG-GATEs基因签名”)