2.2 提取推断的cellchat网络作为数据框架 我们提供一个函数subsetCommunication,以轻松访问推断感兴趣的细胞-细胞通信。例如df.net <- subsetCommunication(cellchat)返回一个数据框架,该数据框架由配体/受体级别的所有推断细胞通信组成。设置slot.name = "netP"可以在信号通路级别访问推断的通信 df.net <- subsetCommunica...
cellchat<-subsetData(cellchat)# subset the expression dataofsignaling genesforsaving computation costfuture::plan("multiprocess",workers=4)#doparallel #>Warning:[ONE-TIMEWARNING]Forkedprocessing('multicore')is disabled #>infuture(>=1.13.0)when runningRfrom RStudio,because it is #>considered unstable...
默认情况下,CellChat使用原始数据(即object@data.signaling),而不是投影数据。如果要使用投影数据,用户应在运行computeCommunProb之前运行projectData函数,然后在运行computeCommunProb时设置raw.use = FALSE。 ##将信号基因的表达矩阵子集化,节省计算成本 cellchat <- subsetData(cellchat) # This step is necessary even...
cellchat <- subsetData(cellchat) # 识别过表达基因 cellchat <- identifyOverExpressedGenes(cellchat) # 识别配体-受体对 cellchat <- identifyOverExpressedInteractions(cellchat) # 将配体、受体投射到PPI网络cellchat <- projectData(cellchat, PPI.human) #计算通信概率推断细胞互作的通信网络 cellchat <- computeCo...
cellchat<- subsetData(cellchat)#必选的step,取上一步CellChatDB.use中信号基因的表达矩阵子集,赋值到cellchat@data.Signaling future::plan('multiprocess', workers = 4)# do parallel #鉴定与每个细胞亚群相关的过表达信号基因: ##基于表达该基因的细胞比例、差异倍数和p值判定。
cellchat <- subsetData(cellchat) 这一步会首先需要选取在上一步选择的interaction database中的基因,这一步并不是一般意义的subset,因为它还会将对应基因的表达矩阵赋值给cellchat@data.Signaling,所以不是可选项,而是必须有的一步 接下来需要识别各个细胞类型过表达(差异)的基因和互作。
load('humanSkin_CellChat.Rdata') dplyr::glimpse(cellchat) #配受体对细胞通讯结果表: df.net <- subsetCommunication(cellchat, slot.name = 'net') head(df.net) #信号通路水平细胞通讯结果表: df.netp <- subsetCommunication(cellchat, slot.name = 'netP') ...
Hi, I am facing troubles in identifyOverExpressedGenes(cellchat) and identifyOverExpressedInteractions(cellchat) functions. I get the same error for both functions: Error in rep(no, length.out = len) : attempt to replicate an object of t...
Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that a
cellchat<-subsetData(cellchat)# do parallel ,根据配置设置future::plan("multiprocess",workers=15)# 识别过表达基因(相当于Seurat的FindMarkers,找每个细胞群中高表达的配受体基因)cellchat<-identifyOverExpressedGenes(cellchat)# 基于CellChatDB数据库,识别过表达的配体-受体相互作对cellchat<-identifyOverExpressedIntera...