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hdng / clonevol

Inferring and visualizing clonal evolution in multi-sample cancer sequencing
GNU General Public License v3.0
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build_tree/infer.clonal.models unused argument error #53

Open nfarnoud opened 2 years ago

nfarnoud commented 2 years ago

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)