Update evodynamics.R

caravagnalab · Sep 21, 2023 · 61bb3e5 · 61bb3e5
1 parent 623c91e
commit 61bb3e5
Showing 1 changed file with 7 additions and 7 deletions.
diff --git a/R/evodynamics.R b/R/evodynamics.R
@@ -632,19 +632,19 @@ get_genome_length = function(fit, exome = FALSE, build = "hg38", karyotypes = NU
 s_posterior = function(fit,N_max,ncells = 1,u = 0,sigma = 1){
 
 
-  if(class(fit$best) == "dbpmmh"){
+  if(class(fit) == "dbpmmh"){
 
-    m = fit$best$data %>% filter(cluster == 'S1',karyotype == "1:1") %>% nrow()
-    mu = mu_posterior(fit$best,ncells = ncells) %>% pull(mean)
-    ccf = (fit$best$data %>% filter(cluster == 'S1',karyotype == "1:1") %>% pull(VAF) %>% mean())*2
-    length_diploid_genome = get_genome_length(fit$best) %>% filter(karyotype == "1:1") %>% 
+    m = fit$data %>% filter(cluster == 'S1',karyotype == "1:1") %>% nrow()
+    mu = mu_posterior(fit,ncells = ncells) %>% pull(mean)
+    ccf = (fit$data %>% filter(cluster == 'S1',karyotype == "1:1") %>% pull(VAF) %>% mean())*2
+    length_diploid_genome = get_genome_length(fit) %>% filter(karyotype == "1:1") %>% 
       pull(length)
 
   }else{
 
-    m = fit$best$data %>% filter(cluster == 'C2') %>% nrow()
+    m = fit$data %>% filter(cluster == 'C2') %>% nrow()
     mu = mutationrate(fit,ncells = ncells)/(2*3*10^9)
-    ccf = (fit$best$data %>% filter(cluster == 'C2') %>% pull(VAF) %>% mean())*2
+    ccf = (fit$data %>% filter(cluster == 'C2') %>% pull(VAF) %>% mean())*2
     length_diploid_genome = 3*10^9
 
 }