detect_startpoint

Function

crisgi_obj.detect_startpoint(symptom_types = ["Symptomatic"])

Detects the start point (CT_time) for samples with specified symptom types and updates the CT_time column in edata.obs. This method filters samples based on the provided symptom types, processes each subject's data, applies a start point detection algorithm, and stores the predicted start time for each subject.

Parameters

Name	Type	Description
symptom_types	list of str	A list of symptom types to filter samples by. Should match values in edata.obs['symptom']. Default is ["Symptomatic"].

Return type

None

Returns

This function does not return a value. It updates the CT_time attribute in the edata.obs DataFrame for each subject matching the specified symptom types.

Attributes Set

• edata.obs['CT_time']: The predicted start time (CT_time) for each subject with the specified symptom types.

Example

# Assume CRISGI is already imported and instantiated as crisgi
# and crisgi.edata is properly initialized

# Detect start points for symptomatic subjects (default)
crisgi.detect_startpoint()

# Detect start points for both symptomatic and asymptomatic subjects
crisgi.detect_startpoint(symptom_types=["Symptomatic", "Asymptomatic"])

# After running, check the predicted CT_time for each subject
print(crisgi.edata.obs[['subject', 'CT_time']].drop_duplicates())