Ha X. Dang
Ha X. Dang
This may be a bug. Could you share some reproducible data and code? Thanks.
I turned out that the bootstrap was not performed, and thus produced such error due to no cellular fraction was estimated. I'll add this to the list of bugs to...
Sorry not yet. Is there a specific reason why you chose not to run the bootstrap?
I don't think min.cluster.vaf is the root cause. What did you use as min.cluster.vaf before?
You meant 0.01, correct? For Pyclone, please see this https://github.com/hdng/clonevol/issues/4. I often see Pyclone results in too many clusters (could be due to parameter setting). Before running clonevol, it is...
I always recommend to run bootstrap. If it does not find a model, non-bootstrap won't find it either. When no model is found for a sample, it indicates clustering issue...
Looking like the cause is that you only have one cluster (hence one clone). I didn't catch this special case but will note this as a bug. Anw, when you...
Could you attach all commands that you ran on this case?
Seems like a bug with cluster ordering. To overcome this, I added these after load('tmp.RData'): clusters = 1:7 names(clusters) = as.character(c(5, 4, 2, 8, 6, 9, 10)) data$cluster = clusters[as.character(data$cluster)]...
Sorry for the late reply. This is a known bug when your cluster ID is not consecutive and founding clone is not 1. I'll release a fix soon. The workaround...