# #设置,回声= FALSE ----------------------------------------------------- suppressPackageStartupMessages({库(ToPASeq)图书馆(石墨 ) }) ## ---- 自由 ------------------------------------------------------------------- 库(ToPASeq) # #——loadAirway ------------------------------------------------------------ 库(气管)数据(气管)# #——processAirway --------------------------------------------------------- airSE < -气道(grep(“^ ENSG”,rownames(气管)))暗(airSE)试验(airSE)[1:4, 1:4] # #——删除0 ---------------------------------------------------------- airSE < -气道[rowSums(化验(airSE)) > 0)暗(airSE)试验(airSE) [1:4, 1:4 ] ## -------------------------------------------------------------------------- 组< - ifelse(气道敏捷= =“泰爱泰党”美元,1,0)表(集团)# #——pwys ------------------------------------------------------------------ 库(石墨)pwys < -通路(物种=“hsapiens”,数据库= " kegg ") [1:5] pwys # #——节点 ----------------------------------------------------------------- 节点(pwys [[1 ]]) ## ---- mapIDs ---------------------------------------------------------------- pwys <石墨::convertIdentifiers (pwys,“运用”)节点(pwys [[1 ]]) ## ---- TopologyGSA ----------------------------------------------------------- 前< -TopologyGSA (pwys化验(airSE),集团类型=“RNASeq”,nperm = 10) res(上)# #——DEGraph --------------------------------------------------------------- 度< -DEGraph (pwys化验(airSE)集团类型=“RNASeq”)res(度)# #——快船 --------------------------------------------------------------- cli <快船(pwys化验(airSE)集团类型=“RNASeq”=“的意思是”方法,nperm = 10) res (cli)结果[[1美元 ]] ## ---- SPIA ------------------------------------------------------------------ spi < -SPIA (pwys化验(airSE)集团类型=“RNASeq”,logFC.th = 1) res (spi) # #——TAPPA ----------------------------------------------------------------- 点击< -TAPPA (pwys化验(airSE)集团类型=“RNASeq”)res (tap) # # - PRS ------------------------------------------------------------------- Prs < -PRS_wrapper (pwys化验(airSE)集团类型=“RNASeq logFC。th = 1, nperm = 10) res (Prs) # #——PWEA ------------------------------------------------------------------ pwe < -PWEA (pwys化验(airSE)集团类型=“RNASeq nperm = 10) res (pwe)