Closed liamxg closed 2 months ago
We have a new manuscript in the works for this very thing. Please stay tuned!
similar to https://github.com/PoonLab/clustuneR? or different?
It's undergoing some final revisions. It is a bit different.
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
@stevenweaver @spond