# #——包括= FALSE --------------------------------------------------------- knitr: opts_chunk美元集(崩溃= TRUE,发表评论 = "#>" ) ## ---- eval = FALSE -------------------------------------------------------------- # 如果(!requireNamespace(“BiocManager”,悄悄地= TRUE)) # install.packages(“BiocManager”)# # BiocManager::安装(“GSEAmining ") ## ---- eval = FALSE -------------------------------------------------------------- # install.packages (devtools) #如果您还没有安装“devtools”包#库(devtools) # devtools:: install_github(“oriolarques / GSEAmining ") ## ---- eval = FALSE -------------------------------------------------------------- # # geneList包含三个特点:# # 1。数字向量:折叠变化或其他类型的数字变量# # 2.命名向量:每个数字都有一个名字，对应基因ID # # 3。排序向量:数量应该# tableTop_p30 < - as.data.frame降序排序(tableTop_p30) # geneList = tableTop_p30[2] #名称(geneList) = as.character (tableTop_p30 [1 ]) ## ---- eval = FALSE -------------------------------------------------------------- # 库(clusterProfiler) # #读取.gmt文件从MSigDB # gmtC2 < -阅读。gmt("gmt files/c2.all.v7.1.symbols.gmt") # gmtC5<-读取。gmt('gmt files/c5.all.v7.1.symbols.gmt') # gmtHALL <-读取。格林尼治标准时间(gmt文件/ h.all.v7.1.symbols.gmt) # # #合并所有的基因集# gmt_all < - rbind (gmtC2、gmtC5 gmtHALL ) ## ---- eval = FALSE -------------------------------------------------------------- # GSEA_p30 < gsea (geneList TERM2GENE = gmt_all nPerm = 1000,pvalueCutoff = 0.5) # # #选择的基因集与特定thershold NES和p.adjust # genesets_sel < - GSEA_p30@result ## ----------------------------------------------------------------------------- # 数据包含在包的数据结构(genesets_sel,包= GSEAmining)宠物猫::(genesets_sel一瞥 ) ## ----------------------------------------------------------------------------- 图书馆(GSEAmining)数据(“genesets_sel”,包= GSEAmining) gs。filt < - gm_filter (genesets_sel p.adj = 0.05, neg_NES = 2.6, pos_NES = 2) # #——设置 -------------------------------------------------------------------- # 创建一个对象,该对象将包含集群的基因集。gs。cl < - gm_clust (gs.filt ) ## ---- fig.height = 7, fig.width = 7 ------------------------------------------- gm_dendplot (gs。filt, gs.cl ) ## ---- fig.height = 7, fig.width = 7 ------------------------------------------- gm_dendplot (gs。filt, gs。cl col_pos =“橙色”,col_neg =‘黑’,矩形= TRUE, dend_len = 20, rect_len = 2 ) ## ---- 消息= FALSE, fig.height = 7, fig.width = 7 -------------------------- gm_enrichterms (gs。filt, gs.cl ) ## ---- 消息= FALSE, fig.height = 7, fig.width = 7 -------------------------- gm_enrichterms (gs。filt, gs。cl, clust = FALSE, col_pos = chocolate3, col_neg = ' skyblue3 ') ## ---- 消息= FALSE, fig.height = 12, fig.width = 7.2 ----------------------- gm_enrichcores (gs。filt, gs.cl ) ## ---- eval = FALSE -------------------------------------------------------------- # gm_enrichreport (gs。filt, gs。cl, output = 'gm_report') ## ----------------------------------------------------------------------------- sessionInfo()