Closed CarlinLiao closed 12 months ago
I've implemented my addition in the pattern of the other analyses, but I'm getting a small error.
One of the custom phenotypes I'm using is a mixture of "simple" and "complex" phenotypes, ["Tumor", "MHCI"]. This causes an error because the phenotype-criteria
API endpoint appears to be only set up to handle "complex" phenotypes, as "Tumor" is processed fine but "MHCI" causes a 500 internal server error. I can work around this, but I would think that this isn't necessarily desired behavior.
Once the above issue is resolved, this is ready to merge.
Look at the other examples, for non-named phenotypes you have to specify a dict of postive_markers
list and negative_markers
list.
Also the sequence of results computed here is supposed to match the manuscript narrative, not just list bulk results. So we should select the ones notable enough to have a sentence about them (and also write that sentence), including in this reproduction script in the same order that they appear in the narrative.
Looks good.
Merge to close #263.