# #设置,包括= FALSE ----------------------------------------------------- knitr: opts_chunk设置(echo = TRUE) knitr:美元:opts_knit设置(进步= FALSE) # #美元——setup1消息= FALSE,结果=“隐藏”,eval = FALSE ------------------------- # #------------------------------------------------------------------------------- # # 安装。包(“BiocManager回购= " http://cran.us.r-project.org ") # BiocManager::安装(“gevaertlab /意大利苦杏酒 ") # # #------------------------------------------------------------------------------- ## ---- AMARETTO_Download1,消息= FALSE,结果=“隐藏”,eval = FALSE ------------- # #------------------------------------------------------------------------------- # # 库(意大利苦杏酒)# TargetDirectory < - tempfile() #数据下载目录# CancerSite < -“LIHC”# DataSetDirectories < - AMARETTO_Download (CancerSite = CancerSite # TargetDirectory = TargetDirectory ) # # #------------------------------------------------------------------------------- ## ---- AMARETTO_Preprocess,消息= FALSE,结果=“隐藏”,eval = FALSE ------------ # #------------------------------------------------------------------------------- # # ProcessedData < - AMARETTO_Preprocess (DataSetDirectories = DataSetDirectories # BatchData = BatchData ) # # #------------------------------------------------------------------------------- ## ---- ProcessedDataLIHC、消息= FALSE结果=“隐藏”,回声= FALSE ------------- 库(意大利苦杏酒)的数据(ProcessedDataLIHC) # #——AMARETTO_Initialize,= '隐藏消息= FALSE,结果 '----------------------- #------------------------------------------------------------------------------- AMARETTOinit < AMARETTO_Initialize (ProcessedData = ProcessedDataLIHC NrModules = 2, VarPercentage = 50 ) #------------------------------------------------------------------------------- ## ---- AMARETTO_Run,消息= FALSE,警告= FALSE,结果= '隐藏 '---------------- #------------------------------------------------------------------------------- AMARETTOresults < - AMARETTO_Run (AMARETTOinit = AMARETTOinit ) #------------------------------------------------------------------------------- ## ---- AMARETTO_EvaluateTestSet,= '隐藏消息= FALSE,结果 '------------------ #------------------------------------------------------------------------------- AMARETTOtestReport < AMARETTO_EvaluateTestSet (AMARETTOresults = AMARETTOresults MA_Data_TestSet = AMARETTOinit MA_matrix_Var美元,RegulatorData_TestSet = AMARETTOinit RegulatorData美元 ) #------------------------------------------------------------------------------- ## ---- AMARETTO_VisualizeModule、消息= FALSE fig.height = 5, fig.width = 7,视网膜= 1 ---- #------------------------------------------------------------------------------- ModuleNr < - 1 #定义模块数量来可视化AMARETTO_VisualizeModule (AMARETTOinit = AMARETTOinit AMARETTOresults = AMARETTOresults ProcessedData = ProcessedDataLIHC ModuleNr = ModuleNr) # #——AMARETTO_HTMLreport消息= FALSE,结果=“隐藏”,eval = FALSE, eval = FALSE ---- # #------------------------------------------------------------------------------- # # gmt_file <执行(“模板/ H.C2CP.genesets.gmt”、包=“意大利苦杏酒”)# AMARETTO_HTMLreport (AMARETTOinit = AMARETTOinit # AMARETTOresults = AMARETTOresults # ProcessedData = ProcessedDataLIHC # hyper_geo_test_bool = TRUE, # hyper_geo_reference = gmt_file # MSIGDB = TRUE ) # # #------------------------------------------------------------------------------- ## ---- eval = TRUE,echo = FALSE,size = 8-------------------------------------- TCGA_codes <- c("BLCA BRCA CESC CHOL COAD ESCA GBM HNSC KIRC KIRP LAML LGG LIHC LUAD LUSC OV PAAD pcg READ SARC STAD THCA THYM UCEC") TCGA_codes <- strsplit(TCGA_codes,split = " ")[[1]] tcga_癌变<- c("膀胱尿路上皮癌"，"乳腺浸润性癌"，"宫颈鳞状细胞癌及宫颈内腺癌"，"胆管癌"，"结肠腺癌"，"食管癌"，"多形胶质母细胞瘤"，“头颈鳞状细胞癌”、“肾肾透明细胞癌”、“肾肾乳头状细胞癌”、“急性髓系白血病”、“脑低级别胶质瘤”、“肝肝细胞癌”、“肺腺癌”、“肺鳞状细胞癌”、“arian浆液性囊腺癌”、“胰腺癌”、“嗜铬细胞瘤及副神经节瘤”、“直肠腺癌”、“肉瘤”、“胃腺癌”、“甲状腺癌”， "thymoma","endometrial carcinoma") tcga_table <- data.frame(TCGA_codes=TCGA_codes,TCGA_cancers=TCGA_cancers) knitr::kable(tcga_table) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()