Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Error in Generating consensus clonal evolution trees across samples #48

Open
qindan2008 opened this issue Dec 25, 2020 · 1 comment
Open

Comments

@qindan2008
Copy link

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 = 'non-parametric',
num.boots = 1000,
random.seed = 1234567,
founding.cluster = 1,
cluster.center = 'median',
ignore.clusters = c(2,3,4),
clone.colors = clone.colors,
min.cluster.vaf = NULL,
sum.p = 0.05,
alpha = 0.05)

Finding consensus models across samples...
Found 1 consensus model(s)
Generating consensus clonal evolution trees across samples...
Error in aggregate.data.frame(mf[1L], mf[-1L], FUN = FUN, ...) :
no rows to aggregate

Here is the input data file of infer.clonal.models, where vaf.col.names=c("M1.vaf" ,"M2.vaf" "P.vaf"), ccf.col.names=c("M1.ccf" ,"M2.ccf" "P.ccf"), sample.groups=c("M","M","P"), names of sample.groups=c("M1","M2","P").
P is primary tumor, both M1 and M2 are metastasis tumor. P and M are from the same patient.

example_data.txt
box

Thank you very much!

@qindan2008
Copy link
Author

When I add sample.names = samples, where samples=c("M1", "M2", "P"), infer.clonal.models turned to be right, no error occurred.

Thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant