how to define the threshold?

[liamxg]

@stevenweaver @spond

[stevenweaver]

We have a new manuscript in the works for this very thing. Please stay tuned!

[liamxg]

similar to https://github.com/PoonLab/clustuneR? or different?

[stevenweaver]

It's undergoing some final revisions. It is a bit different.

[spond]

Dear @liamxg,

If you use hivnetworkcsv (a part of https://github.com/veg/hivclustering), which is a component of HIV-TRACE, you can use --threshold auto option.

For example, using the data which ships with hivclustering

$hivnetworkcsv -i examples/tn93-0.03.csv -f plain -t auto
....
ERROR : Could not automatically determine a distance threshold; no sufficiently strong outlier, best guess 0.01726 (score 1.07156)

In this particular case, the tool is suggesting the threshold of 0.01726, even though it's not confident enough to just use it (it will be in other cases, as the upcoming manuscript will detail).

So next, you could use

$hivnetworkcsv -i examples/tn93-0.03.csv -f plain -t 0.01726

Cheers, Sergei