Hello,
It appears thatbuild_tree is calling infer.clonal.models with an argument called post.sample.col, however, this does not exist in infer.clonal.models, so it generates an error. When I run a copy of build_tree with this argument commented out, my model(s) are successfully generated.
Best,
Noushin
models = infer.clonal.models(
variants = clonevol_in,
cluster.col.name = "cluster",
ccf.col.names = sample_ids,
# sample.groups = sample.groups,
post.sample.col = post.sample.col, #### THIS ARG IS NOT DEFINED
cancer.initiation.model = clonal.model,
subclonal.test = 'bootstrap',
subclonal.test.model = 'non-parametric',
num.boots = 1000,
founding.cluster = 1,
cluster.center = 'mean',
ignore.clusters = NULL,
clone.colors = clone.colors,
min.cluster.vaf = min.cluster.vaf,
# min probability that CCF(clone) is non-negative
sum.p = sum.p,
random.seed = rand.seed,
# alpha level in confidence interval estimate for CCF(clone)
alpha = 0.05)
Hello, It appears that
build_tree
is callinginfer.clonal.models
with an argument called post.sample.col, however, this does not exist in infer.clonal.models, so it generates an error. When I run a copy of build_tree with this argument commented out, my model(s) are successfully generated.Best, Noushin