# #——包括= TRUE,结果=“隐藏”,消息= FALSE,警告= FALSE ------------------ 库(MultiAssayExperiment)库(S4Vectors ) ## ----------------------------------------------------------------------------- 数据(miniACC) miniACC ## ----------------------------------------------------------------------------- colData (miniACC) [1:4,1:4)表(miniACC美元竞赛 ) ## ----------------------------------------------------------------------------- 实验(miniACC ) ## ----------------------------------------------------------------------------- sampleMap (miniACC ) ## ----------------------------------------------------------------------------- 元数据(miniACC ) ## ---- 结果= '隐藏 '---------------------------------------------------------- miniACC [c(“MAPK14”、“IGFBP2”),] ## ---- 结果= '隐藏 '---------------------------------------------------------- stg4 < - miniACC pathologic_stage美元= =“四期”#删除NA值向量miniACC [, stg4 & ! is.na stg4 ), ] ## ---- 结果= '隐藏 '---------------------------------------------------------- RNASeq2GeneNorm miniACC(,。 "] ## ----------------------------------------------------------------------------- miniACC [l][1] #或等价,RNASeq2GeneNorm miniACC[[” "]] ## ----------------------------------------------------------------------------- 总结(complete.cases (miniACC )) ## ----------------------------------------------------------------------------- accmatched = intersectColumns (miniACC ) ## ----------------------------------------------------------------------------- colnames (accmatched ) ## ----------------------------------------------------------------------------- accmatched2 < - intersectRows (miniACC [,,c(“RNASeq2GeneNorm”、“gistict”、“突变”)])rownames (accmatched2 ) ## ----------------------------------------------------------------------------- 类(试验(miniACC )) ## ----------------------------------------------------------------------------- 化验(miniACC ) ## ----------------------------------------------------------------------------- longFormat (miniACC [c(“TP53”、“CTNNB1”),),colDataCols = c(“vital_status”,“days_to_death ")) ## ----------------------------------------------------------------------------- wideFormat (miniACC [c(“TP53”、“CTNNB1”),),colDataCols = c(“vital_status”、“days_to_death ")) ## ----------------------------------------------------------------------------- MultiAssayExperiment(实验=实验(miniACC) colData = colData (miniACC) sampleMap = sampleMap (miniACC),元数据的元数据(miniACC = )) ## ----------------------------------------------------------------------------- miniACC2 < - c (miniACC log2rnaseq = log2(化验(miniACC) RNASeq2GeneNorm美元),mapFrom = 1 l)化验(miniACC2 ) ## ----------------------------------------------------------------------------- 库(UpSetR) upsetSamples (miniACC ) ## ----------------------------------------------------------------------------- suppressPackageStartupMessages({库(生存)库(survminer)}) coldat < - as.data.frame (colData (miniACC)) coldat $ y < - Surv (miniACC days_to_death美元,miniACC vital_status美元)colData (miniACC) < - DataFrame (coldat ) ## ----------------------------------------------------------------------------- miniACC < - miniACC [, complete.cases (coldat $ y)] coldat <——(colData (miniACC),“data.frame ") ## ----------------------------------------------------------------------------- 符合< - survfit (y ~ pathology_N_stage, data = coldat) ggsurvplot(健康,data = coldat、风险。表= TRUE ) ## ----------------------------------------------------------------------------- wideacc < - wideFormat (miniACC EZH2,,, colDataCols = c(“vital_status”、“days_to_death”,“pathology_N_stage”))wideacc < - $ y Surv (wideacc days_to_death美元,wideacc vital_status美元)头(wideacc ) ## ----------------------------------------------------------------------------- coxph (Surv (days_to_death vital_status) ~ gistict_EZH2 + log2 (RNASeq2GeneNorm_EZH2) + pathology_N_stage, data=wideacc) ## ----------------------------------------------------------------------------- sessionInfo()