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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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Interpretations of results from infer.clonal.model #30

Open huiyao25 opened 5 years ago

huiyao25 commented 5 years ago

Hello,

I am a new user for clonevol package, which provides a set of very useful analyses and visualizations for clonal evolution. I tried to find the explanations of results from the functions of infer.clonal.model, which produces a long list of results. For an example,

names(clone_mod_t6_7_8_9) [1] "models" "matched" "num.matched.models" "num.pruned.trees" "variants"
[6] "params"

I guessed that “models” is about the individual samples. “matched” is about the merged models across samples. Then, for the list of results from “matched”, where could I find some explanations of them?

names(clone_mod_t6_7_8_9$matched) [1] "index" "merged.trees" "merged.traces"
[4] "scores" "probs" "clone.ccf.pvalues"
[7] "trimmed.merged.trees" "trimmed.merged.trees.map"

For examples, “sample.with.cell.frac.ci” or “sample.with.nonzero.cell.frac.ci” is labeled in the bell plot. What are exact meaning for them?

Any help is highly appreciated.

Best,

Hui