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iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Make susceptibility calls based on median coverage in mixed. #24

Closed Phelimb closed 9 years ago

Phelimb commented 9 years ago

If we have a sample that is 90x Aureus and 10x epi and we see:

"mecA" :{ "per_cov": "100", "median_cov": "10", "induced_resistance": "Methicillin" }, "blaZ" :{ "per_cov": "100", "median_cov": "95", "induced_resistance": "Penicillin" },

It would be nice if we called confident penicillin R but methicillin S.

Phelimb commented 9 years ago

I've realised that this isn't particularly clear. In this sample, although we call EPI as mixed, we call METH as R despite the fact that the MEC is very likely coming from the EPI not the AUREUS.

iqbal-lab commented 9 years ago

So solution 1

Currently the app throws a dialog if it is mixed and refuses to show resistance, so that's fine The Staph app does not have a Species tab, and I don't think we can modify the UI to do that quickly. So we release with this.

SOlution 2 Ideally we to throw a dialog saying "warning" rather than error, and then show all results, maybe going to species tab first if mixed/non-TB/Staph

On 12 January 2015 at 11:25, Phelim Bradley notifications@github.com wrote:

I've realised that this isn't particularly clear. In this sample, although we call EPI as mixed, we call METH as R despite the fact that the MEC is very likely coming from the EPI not the AUREUS.

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/myKrobe-predictor/issues/24#issuecomment-69556988 .

iqbal-lab commented 9 years ago

Out of date