how to translate the copykat results to inferCNV i6 HMM (the six-state CNV model)

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
25/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Tech stack
r
Domain
bioinformatics

Research direction

Start by reviewing how copykat represents CNV results and how inferCNV defines its six i6HMM states. No file, test, or entry point is named in the issue. Done means documenting whether and how copykat results map to the listed inferCNV states, including the handling of values above two copies.

Written by the indexing model from the issue text.

Description

Hi,
thanks for the cool software!
I would like to ask how to connect the copykat results into i6HMM state in inferCNV? Thanks!
0x: complete loss
0.5x: loss of one copy
1x: neutral
1.5x: addition of one copy
2x: addition of two copies
3x: essentially a placeholder for >2x copies but modeled as 3x.

Dominant language
R
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305
Forks
66
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  4. Open a pull request that references the issue number.

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