# #——style-knitr eval = TRUE,呼应= FALSE,结果= '飞机 '-------------------- BiocStyle:乳胶 () ## ---- 选择,包括= FALSE,回声= FALSE --------------------------------------- knitr: opts_chunk美元集(和合= TRUE, eval = TRUE,缓存= FALSE, resize.width =“0.45 \ \ textwidth”,fig.align =‘中心’,整洁= FALSE,消息= FALSE,警告= FALSE) # #——安装,eval = FALSE --------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) {# install.packages (BiocManager) #} # BiocManager::安装(“泛太平洋伙伴关系 ") ## ---- 包 --------------------------------------------------------------- 图书馆(“泛太平洋伙伴关系 ") ## ---- load_2d_data ---------------------------------------------------------- 数据(panobinostat_2DTPP_smallExample、包= " TPP ") ## ---- head_2d_data,eval = TRUE ----------------------------------------------- config_tpp2d < - panobinostat_2DTPP_config data_tpp2d < - panobinostat_2DTPP_data config_tpp2d data_tpp2d % > % str(1) # #——colnames_Pano eval = TRUE ---------------------------------------------- data_tpp2d X020466美元% > % colnames # #——ttp2dworkflow eval = TRUE,警告= FALSE ----------------------------- tpp2dResults < - analyze2DTPP (configTable = config_tpp2d、数据= data_tpp2d compFc = TRUE, idVar =“代表”,intensityStr = "sumionarea_protein_"， nonZeroCols = "qusm"， addCol = "clustername"， methods = "doseResponse"， createReport = "none") tpp2dResults %>% mutate_if(is。character, factor) %>% summary ## ----ttp2dDataImport2, eval=TRUE, warning=FALSE---------------------------- data2d <- tpp2dImport(configTable = config_tpp2d, data = data_tpp2d, idVar = "representative"， intensityStr = "sumionarea_protein_"， nonZeroCols = "qusm"， addCol = "clustername") head(data2d) attr(data2d， "importSettings") ## ----ttp2dComputeFC2, eval=TRUE-------------------------------------------- fcData2d <- tpp2dComputeFoldChanges(data = data2d) ## ----head_fold_changes2，eval = TRUE ----------------------------------------- 头(fcData2d) # #——ttp2dDoMedianNorm2 eval = TRUE ----------------------------------------- normData2d < - tpp2dNormalize(数据= fcData2d)头(normData2d) # #——tpp2dRunTPPCCR2 eval = TRUE,警告= FALSE ----------------------------- ccr2dResults < - tpp2dCurveFit(数据= normData2d) # #——tpp2dPlotGoodCurves eval = TRUE,警告= FALSE ------------------------- drPlots < - tpp2dCreateDRplots (data = ccr2dResults type = "好 ") ## ---- plotCurve2,eval=TRUE, fig.height=6, fig.width=7.5-------------------- #查找HDAC2的IPI id(在列代表中):IPI_id_HDAC2 <- unique(filter(ccr2dResults, clustername == "HDAC2")$representative) #显示相应的plot:drPlots[[IPI_id_HDAC2]] ## ----plotSingleCurves, eval=TRUE, figeshow ='hide'， figeheight =6, figewidth =7.5---- drPlotsByTemperature <- tpp2dCreateDRplots(data = ccr2dResults, type = "single") drPlotsByTemperature[[IPI_id_HDAC2]][["54"]] ## ----result_path_2DTPP, eval=TRUE ---------------------------------------- resultPath = file.path(getwd()， 'Panobinostat_Vignette_Example_2D') if (!file.exists(resultPath)) dir。创建(resultPath,递归= TRUE) # #——generateReferenceInputData eval = FALSE,警告= FALSE --------------- # 数据(“hdacTR_smallExample”)# trConfig < - hdacTR_config [1:2,] % > % # dplyr::选择(-dplyr:匹配(“比较”))# # trConfig # #——generateReferenceOject eval = FALSE,警告= FALSE ------------------- # tpp2dCreateTPPTRreference (trConfigTable = trConfig # trDat = hdacTR_data [1:2], # resultPath = resultPath # outputName =“desired_file_name”,# createFCboxplots = FALSE) ## ----pE50plots, eval = TRUE, warning = FALSE------------------------------- #设置HepG2 TR参考数据集的系统路径:trRef <- file.path(system. path)file("data"， package="TPP")， "TPPTR_reference_results_HepG2.RData") plotData <- ccr2dResults %>% filter(clustername == "HDAC2") pEC50QC_HDAC1 <- tpp2dPlotQCpEC50(resultTable = plotData, resultPath = NULL, trRef = trRef, idVar =" representative") pEC50QC_HDAC1[[1]] ## ----qcHists, eval =FALSE, warning=FALSE---------------------------------- # tpp2dPlotQChist(configFile = config_tpp2d， # resultTable = ccr2dResults， # resultPath = resultPath， # trRef = trRef， # idVar =" representative")