## ----load package, message=FALSE---------------------------------------------- library(LinTInd) ## ----message=FALSE------------------------------------------------------------ data<-paste0(system.file("extdata",package = 'LinTInd'),"/CB_UMI") fafile<-paste0(system.file("extdata",package = 'LinTInd'),"/V3.fasta") cutsite<-paste0(system.file("extdata",package = 'LinTInd'),"/V3.cutSites") celltype<-paste0(system.file("extdata",package = 'LinTInd'),"/celltype.tsv") data<-read.table(data,sep="\t",header=TRUE) ref<-ReadFasta(fafile) cutsite<-read.table(cutsite,col.names = c("indx","start","end")) celltype<-read.table(celltype,header=TRUE,stringsAsFactors=FALSE) ## ----------------------------------------------------------------------------- head(data,3) ref cutsite head(celltype,3) ## ----find indels and generate array-form strings, message=FALSE--------------- scarinfo<-FindIndel(data=data,scarfull=ref,scar=cutsite,indel.coverage="All",type="test",cln=1) scarinfo<-IndelForm(scarinfo,cln=1) ## ----IndelIdents, message=FALSE----------------------------------------------- cellsinfo<-IndelIdents(scarinfo,method.use="umi.num",cln=1) ## ----IndelPlot---------------------------------------------------------------- IndelPlot(cellsinfo = cellsinfo) ## ----TagProcess--------------------------------------------------------------- tag<-TagProcess(cellsinfo$info,Cells=celltype) ## ----TagDist------------------------------------------------------------------ tag_dist=TagDist(tag,method = "Jaccard") tag_dist ## ----BuildTree---------------------------------------------------------------- treeinfo<-BuildTree(tag) ## ----PlotTree----------------------------------------------------------------- plotinfo<-PlotTree(treeinfo = treeinfo,data.extract = "TRUE",annotation = "TRUE") plotinfo$p ## ----sessionInfo, echo=TRUE--------------------------------------------------- sessionInfo()