How to use?

Config (yaml file)

  1. Define a disease

  2. Define disease cases

  • cases can be subdivided by severity, age, and gender (sex)

  • or single cases

  1. For each case one must have the LFC table

  2. Configure the all params using mtp_MB_01_config.ipynb

  3. Chenk if the basic configuration works

  4. Define the new LFC and FDR cutoffs manually or run BCA (if available)

Examples

DPC and BCA must be able to split each case and define the disease, severity, age, and gender.

COVID-19:

  • g1: assymptomatic

  • g2a: mild

  • g2b: moderate

  • g3: severe

Cases:

case_list = [‘g1_male’, ‘g1_female’, ‘g2a_male’, ‘g2a_female’, ‘g2b_male’, ‘g2b_female, ‘g3_male_adult’, ‘g3_female_adult’, ‘g3_male_elder’, ‘g3_female_elder’]

MB:

  • WNT

  • SHH ~ Sonic hedgehog

  • G3

  • G4

Cases:

case_list = [‘WNT’, ‘G4’] # our study has only WNT and G4.