# # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # RNAseq = RNAseq[应用(RNAseq 1函数(x)和(x = = 0)) 0)= 1 # # #计算淋巴细胞基因的意义衡量得分(lscore) -韦尔奇t # GS_lscore = t(酸式焦磷酸钠(1:ncol (WGCNA_matrix2),函数c (x) (t.test (WGCNA_matrix2 [x] ~ lscore, var.equal = F) $ p。价值,# t.test (WGCNA_matrix2 [x] ~ lscore, var.equal = F)估计[1],美元# t.test (WGCNA_matrix2 [x] ~ lscore, var.equal = F)估计美元[2]# GS_lscore = cbind (GS)))。lscore、abs (GS_lscore [2]——GS_lscore [3])) # colnames (GS_lscore) = c (‘p_value’,‘mean_high_lscore’,‘mean_low_lscore’, #“effect_size(得分高低)');rownames (GS_lscore) = colnames (WGCNA_matrix2) # # - - - - - eval = FALSE - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # #参考基因= 5000前疯狂基因# ref_genes = colnames (WGCNA_matrix2) # # #创建数据框架去分析#库(org.Hs.eg.db) # = toTable (org.Hs.egGO);符号= toTable (org.Hs.egSYMBOL) # GO_data_frame = data.frame(去go_id美元,证据,美元符号$符号(匹配(gene_id美元,象征gene_id美元)])# # # #创建GOAllFrame对象库(AnnotationDbi) # GO_ALLFrame = GOAllFrame (GOFrame (GO_data_frame有机体=“智人”))# # #创建基因集#库(GSEABase) # gsc < - GeneSetCollection (GO_ALLFrame setType = GOCollection()) # # #执行去富集分析和结果保存到列表——这使花几分钟#库(GEOstats) # GSEAGO =向量(“列表”,长度(独特(模块)))#,(我在0(长度(独特(模块))1)){# GSEAGO [[i + 1]] =总结(hyperGTest (GSEAGOHyperGParams (name =“智人”,# GeneSetCollection = gsc geneIds = colnames (RNAseq)(模块= =我),# universeGeneIds = ref.genes本体=“英国石油公司”,pvalueCutoff = 0.05, #条件= FALSE, testDirection = ' / '))) #打印(i) #} # # cutoff_size = 100 # # GO_module_name =代表(NA、长度(独特(模块)))#,(我在1:长度(独特(模块))){# GO.module.name[我]= # GSEAGO[[我]][GSEAGO[[我]]美元大小