clonevol
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hdng
Inferring and visualizing clonal evolution in multi-sample cancer sequencing
Hello, I get the following error when running infer.clonal.models(). Can you please help me fix this? Finding consensus models across samples... Found 1 consensus model(s) Generating consensus clonal evolution trees...
Hi, Dang, H. X., I'm trying to use Clonevol, but I cannot get consensus model when I tried to run "_infer.clonal.model_s". In this example, I have 6 samples (3 primary,...
Dear Ha X. Dang, Hello, I am trying to analyze clonal evolution using PyClone and ClonEvol. I have two WES samples from one patient. When I followed the manual, I...
Hello, When I run infer.clonal.models, an error occurred. y = infer.clonal.models(variants = data, cluster.col.name = 'cluster', vaf.col.names = vaf.col.names, ccf.col.names = ccf.col.names, sample.groups = sample.groups, cancer.initiation.model='monoclonal', subclonal.test = 'bootstrap', subclonal.test.model...
Hello, I have 10 pairs of samples. They're paired primary and metastasis tumors, but none of them have normal controls. Can variants called by mutect2 or other snp callers be...
First time User. Step by step to run the code in Tutorial by Dr. Dang, but some errors always come up. Need help! Thanks in advance. R version 4.0.2 (2020-06-22)...
I think I'm missing something really basic here but I can't make this function to work. it does not find it. Error in estimate.clone.vaf(clonevol_model$variants, vaf.col.names = vaf.col.names) : could not...
Warning messages: 1: `fun.y` is deprecated. Use `fun` instead. 2: `show_guide` has been deprecated. Please use `show.legend` instead. 3: `fun.y` is deprecated. Use `fun` instead. 4: `show_guide` has been deprecated....
In the function infer.clonal.models(), there is the option to specify cluster.col.name (default = 'cluster'), which I've been naming 'cluster_id'. But in the code where infer.clonal.models() calls on generate.boot, cluster.col.name isn't...
Hi I have 50 patients who have responded to chemotherapy from which 17 samples are pre-treatment biopsies and 33 patients post-treatment resections. The pre and post samples are not matched....
