## ----cellCellSimulate_Default, echo=TRUE-------------------------------------- suppressPackageStartupMessages(library("scTensor")) sim <- cellCellSimulate() ## ----cellCellSimulate_Setting, echo=TRUE-------------------------------------- # Default parameters params <- newCCSParams() str(params) # Setting different parameters # No. of genes : 1000 setParam(params, "nGene") <- 1000 # 3 cell types, 20 cells in each cell type setParam(params, "nCell") <- c(20, 20, 20) # Setting for Ligand-Receptor pair list setParam(params, "cciInfo") <- list( nPair=500, # Total number of L-R pairs # 1st CCI CCI1=list( LPattern=c(1,0,0), # Only 1st cell type has this pattern RPattern=c(0,1,0), # Only 2nd cell type has this pattern nGene=50, # 50 pairs are generated as CCI1 fc="E10"), # Degree of differential expression (Fold Change) # 2nd CCI CCI2=list( LPattern=c(0,1,0), RPattern=c(0,0,1), nGene=30, fc="E100") ) # Degree of Dropout setParam(params, "lambda") <- 10 # Random number seed setParam(params, "seed") <- 123 # Simulation data sim <- cellCellSimulate(params) ## ----input, echo=TRUE--------------------------------------------------------- dim(sim$input) sim$input[1:2,1:3] ## ----LR, echo=TRUE------------------------------------------------------------ dim(sim$LR) sim$LR[1:10,] sim$LR[46:55,] sim$LR[491:500,] ## ----celltypes, echo=TRUE----------------------------------------------------- length(sim$celltypes) head(sim$celltypes) table(names(sim$celltypes)) ## ----sessionInfo, echo=FALSE-------------------------------------------------- sessionInfo()