hklarner/detection_of_markers_for_discrete_phenotypes

A place to discuss the paper "Detection of markers for discrete phenotypes".

detection_of_markers_for_discrete_phenotypes's Issues

CSV export not correctly described in the help document

Hello,

According to biomarkers problem-solve -h, the command below should create a csv. I could not observe this behaviour
biomarkers problem-solve --problem toy_problem.json --forbidden x4,x5 --marker-size-max 5 --markers toy_markers.csv

toy_problem.json

Example fails

biomarkers problem-create --problem emt_problem.json --bnet selvaggio_emt --phenotype AJ_b1=0,AJ_b2=0 fails for me with following error message
/home/td/.local/lib/python3.10/site-packages/pydantic/_internal/_config.py:334: UserWarning: Valid config keys have changed in V2: 'keep_untouched' has been renamed to 'ignored_types' warnings.warn(message, UserWarning) failed to create marker detection problem: error=1 validation error for Problem phenotype_components Field required [type=missing, input_value={'primes': {'AJ_b1': [[{'...subspace': {0: 0, 1: 0}}, input_type=dict] For further information visit https://errors.pydantic.dev/2.7/v/missing

Markers-factorize throws error

Hello I encountered another error,

Calculating a marker set factorization throws an error (See screenshot). The factorization is still being done (I think) but the program does not exit properly but instead throws an error. The documentation shows that pdfs should get created. This is not happening.

Thanks again for your time.

Boolean net in bnet format (Its the toy example from the markers paper)

x1, x2
x2, x1
x3, x4
x4, x3
x5, x2 & x4
x6, x2 | (!x2 & !x3)