immuneSIM VDJ frequencies not matching

[niccolocard99]

Hi

I am using immuneSIM to simulate a repertoire with an altered usage of V , D and J genes, but the resulting repertoire V,D,J frequencies do not match the ones I gave in input.

I have altered the frequencies by copying the default "list_germline_genes_allele_01" and substituting the values in the column "frequency". In the example below I only show the J genes

vdj_list <- list_germline_genes_allele_01
vdj_list$hs$ig$h$J[,"frequency"] <- c( 0.01280559,0.02328289 ,0.08614668, 0.29569267, 0.10942957 ,0.47264261)

sim_repertoire <- immuneSIM(
                number_of_seqs = 500  ,
                vdj_list = vdj_list,
                species = "hs",
                receptor = "ig",
                chain = "h",
                verbose=TRUE,
                shm.mode = "none",
                shm.prob = 7/350,
                freq_update_time=c(250 ),
                vdj_noise = 0,                
                max_cdr3_length = 45)

But when i check the frequencies of J gene, they are quite different from the ones that i set.

> prop.table(table(sim_repertoire$j_call))

IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.016 0.032 0.074 0.346 0.122 0.410 

I tried to with number_of_seqs of 5000,10.000, 50.000 , but the results are the same.

Thanks in advance for the support :)

P.S: I also tried to change the freq_update_time paramter, but the result changes only slightly

freq_update_time 300
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.010 0.034 0.062 0.350 0.130 0.414

freq_update_time 350
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.024 0.040 0.068 0.326 0.146 0.396 

freq_update_time 400
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.020 0.036 0.060 0.350 0.142 0.392 

freq_update_time 200
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.016 0.028 0.068 0.328 0.140 0.420

freq_update_time 150
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.016 0.028 0.062 0.342 0.130 0.422 

freq_update_time 100
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.012 0.034 0.058 0.342 0.130 0.424

freq_update_time 50
IGHJ1 IGHJ2 IGHJ3 IGHJ4 IGHJ5 IGHJ6 
0.024 0.018 0.062 0.340 0.136 0.420