I encountered an issue when running the tree-building process with min_cluster_size = 4. While the process works fine for min_cluster_size = 5, some cases fail when using a value of 4. However, not all cases encounter this issue. What is the possible cause? The error occurs during the tree-building step with the following message:
Starting Tree Building
Following parameters used for tree building:
[,1]
sampleID "case_id"
prefix "prefix"
generalSave "/path/to/case_id/results/conipher//Trees//"
ccf_buffer "10"
pval_cutoff "0.01"
use_boot "TRUE"
merge_clusters "TRUE"
correct_cpn_clusters "TRUE"
adjust_noisy_clusters "FALSE"
adjust_noisy_clusters_prop "0.05"
min_ccf "0.01"
min_cluster_size "4"
Determining nesting of clusters
Loading required package: boot
[1] "Calculating cluster confidence intervals using bootstrapping"
[1] "Number of bootstrapping replicates: 5000"
[1] "Number of bootstrapping replicates: 5000"
[1] "Number of bootstrapping replicates: 5000"
The following nesting identified:
1 16 10 11 2 7 14 18 6 8 15 4 9 17 3 12 13 5 19
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
3 1 1 1 1 1 1 0 1 1 1 0 1 1 0 0 0 0 0 0
4 1 1 1 1 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0
5 1 1 1 1 1 1 0 0 1 0 0 0 0 0 0 1 0 0 0
6 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0
7 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
8 1 1 1 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
9 1 1 1 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0
10 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
11 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
12 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
13 1 1 1 1 1 1 0 0 1 0 0 0 0 0 0 0 0 0 0
14 1 0 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
15 1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
16 1 0 0 1 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0
17 1 1 1 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0
18 1 1 0 1 0 0 1 0 0 0 1 0 0 1 0 0 0 0 0
19 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 1 0 0
[1] "Calculating cluster confidence intervals using bootstrapping"
[1] "Number of bootstrapping replicates: 5000"
Checking for cluster merging
Checking for chromosome clustered clusters
No clusters removed
Building trees...Error in rbind(edgelist_new, cbind(essential_parents, terminal_node)) :
number of columns of matrices must match (see arg 2)
Calls: conipher_run ... treebuilding_run -> grow.trees -> prune.tree_test -> rbind
In addition: There were 50 or more warnings (use warnings() to see the first 50)
Execution halted
Using min_cluster_size = 5 works without issues.
Starting Tree Building
Following parameters used for tree building:
[,1]
sampleID "case_id"
prefix "prefix"
generalSave "/path/to/case_id/results/conipher//Trees//"
ccf_buffer "10"
pval_cutoff "0.01"
use_boot "TRUE"
merge_clusters "TRUE"
correct_cpn_clusters "TRUE"
adjust_noisy_clusters "FALSE"
adjust_noisy_clusters_prop "0.05"
min_ccf "0.01"
min_cluster_size "5"
Determining nesting of clusters
Loading required package: boot
[1] "Calculating cluster confidence intervals using bootstrapping"
[1] "Number of bootstrapping replicates: 5000"
[1] "Number of bootstrapping replicates: 5000"
[1] "Number of bootstrapping replicates: 5000"
The following nesting identified:
1 10 11 2 8 7 5 4 9 12 3 6 13
1 0 0 0 0 0 0 0 0 0 0 0 0 0
2 1 1 1 0 0 0 0 0 0 0 0 0 0
3 1 1 1 1 1 1 1 1 1 0 0 0 0
4 1 1 1 1 0 0 1 0 0 0 0 0 0
5 1 1 1 0 0 0 0 0 0 0 0 0 0
6 1 1 1 1 1 1 0 0 0 1 0 0 0
7 1 1 1 1 1 0 0 0 0 0 0 0 0
8 1 1 1 0 0 0 0 0 0 0 0 0 0
9 1 1 0 0 1 0 0 0 0 0 0 0 0
10 1 0 0 0 0 0 0 0 0 0 0 0 0
11 1 0 0 0 0 0 0 0 0 0 0 0 0
12 1 0 0 0 0 0 0 0 0 0 0 0 0
13 1 1 1 1 1 1 0 0 0 0 0 0 0
[1] "Calculating cluster confidence intervals using bootstrapping"
[1] "Number of bootstrapping replicates: 5000"
Checking for cluster merging
Checking for chromosome clustered clusters
No clusters removed
Building trees...
Testing mutation removal:
5/167 mutations (2.99%)
6/167 mutations (3.59%)
7/167 mutations (4.19%)
8/167 mutations (4.79%)
10/167 mutations (5.99%)
11/167 mutations (6.59%)
12/167 mutations (7.19%)
13/167 mutations (7.78%)
14/167 mutations (8.38%)
15/167 mutations (8.98%)
16/167 mutations (9.58%)
17/167 mutations (10.2%)
18/167 mutations (10.8%)
19/167 mutations (11.4%)
20/167 mutations (12%)
21/167 mutations (12.6%)
22/167 mutations (13.2%)
23/167 mutations (13.8%)
24/167 mutations (14.4%)
25/167 mutations (15%)
26/167 mutations (15.6%)
27/167 mutations (16.2%)
28/167 mutations (16.8%)
29/167 mutations (17.4%)
30/167 mutations (18%)
31/167 mutations (18.6%)
32/167 mutations (19.2%)
33/167 mutations (19.8%)
----------------
Removing the following clusters:
12 11 3 2
Total mutations removed: 33 [1] "3"
[1] "12"
I encountered an issue when running the tree-building process with
min_cluster_size = 4. While the process works fine formin_cluster_size = 5, some cases fail when using a value of 4. However, not all cases encounter this issue. What is the possible cause? The error occurs during the tree-building step with the following message:Using
min_cluster_size = 5works without issues.