Rscripts_For_Simulation/Sim12.R

In alexyermanos/Echidna: Single Cell Immune Repertoire and Transcriptome Simulation

#class igM+ igG dominate + little other
class_switch_prob_mus[class_switch_prob_mus>0]<-0
class_switch_prob_mus[1,3]<-0.01
class_switch_prob_mus[1,4]<-0.01
class_switch_prob_mus[1,5]<-0.01
class_switch_prob_mus[1,2]<-0.001
class_switch_prob_mus[1,6]<-0.001
class_switch_prob_mus[1,7]<-0.001
class_switch_prob_mus[7,1]<-0.1
#trans naive B cells, memory B cells, PCs, and GCs
trans_switch_prob_b[trans_switch_prob_b>0]<-0
trans_switch_prob_b[1,3]<-0.0001
trans_switch_prob_b[1,2]<-0.0001
trans_switch_prob_b[2,3]<-0.05
trans_switch_prob_b[3,4]<-0.01
trans_switch_prob_b[4,3]<-0.01
#
expanded_p<-simulate_repertoire(initial.size.of.repertoire = 50,
                                duration.of.evolution = 30,
                                vdj.branch.prob = 0.1,
                                cell.division.prob = c(0.2,0.2,0.5),
                                class.switch.prob = class_switch_prob_mus,
                                transcriptome.switch.prob = trans_switch_prob_b,
                                max.cell.number = 5000,
                                max.clonotype.number = 5000,
                                complete.duration=T,
                                clonal.selection =T,
                                death.rate = 0,
                                transcriptome.on = T,
                                SHM.nuc.prob = 0.00001,
                                sequence.selection.prob = 0.2,
                                transcriptome.switch.selection.dependent = T,
                                class.switch.selection.dependent = T,
                                transcriptome.switch.independent = T
)