# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,评论 = "#>" ) 库(BiocStyle) # #——load-ges ----------------------------------------------------------------- 库(GeneExpressionSignature) # #——get-ranklist消息= FALSE ----------------------------------------------- # 如果你有网络访问# GSM118720 < - getGEO (GSM118720) # GSM118721 < - getGEO (GSM118721)如果(要求(GEOquery)){#治疗基因GSM118720 < - getGEO(文件名=系统。文件(“extdata / GSM118720。GSM118721 <- getGEO(filename=system. exe);文件(“extdata / GSM118721。--- as.matrix(as.numeric(Table(GSM118721)[， 2])) ranked_list <- as.matrix(as.numeric(Table(GSM118720)[， 2])) ranked_list <- getRLs(control, treatment)} ## ----sample-data-------------------------------------------------------------- data(exampleSet) show(exampleSet) exprs(exampleSet)[c(1:10)， c(1:3)] levels(as(phenoData(exampleSet)， "data.frame")[，1 ]) ## ---- rank-merge --------------------------------------------------------------- MergingSet < - RankMerging (exampleSet“枪兵”,加权= TRUE)显示(MergingSet) # #——gsea --------------------------------------------------------------------- ds < - ScoreGSEA (MergingSet, 250,“avg”)ds(1:5, 1:5) # #——sig-dis ------------------------------------------------------------------ SignatureDistance (exampleSet SignatureLength = 250, MergingDistance =“枪兵”,ScoringMethod =“GSEA”,ScoringDistance =“avg加权= TRUE ) ## ---- merge-detail ------------------------------------------------------------- MergingSet < - RankMerging (exampleSet“枪兵”,加权= TRUE) (MergingSet) # #——gsea-detail -------------------------------------------------------------- ds < - ScoreGSEA (MergingSet, 250,“avg”)ds(1:5, 1:5) # #——pgsea-detail ------------------------------------------------------------- ds < - ScorePGSEA (MergingSet, 250,“avg”)ds(1:5, 1:5) # #——集群 ------------------------------------------------------------------ 如果需要(apcluster)){图书馆(apcluster) clusterResult < apcluster (1 - ds)显示(clusterResult)} # #——cluster-graph回声= FALSE ------------------------------------------------- knitr: include_graphics(“cluster.png ") ## ---- 会话 ------------------------------------------------------------------ sessionInfo ()