Cohort Pathways
Last updated
Last updated
Cohort Pathways in Atlas helps you understand the sequence of events in Target Cohorts.
The Cohort Pathways allows you to study the sequence of transitions between Event Cohorts among the people in the Target Cohorts. Events of interest include treatments, procedures, medicines, or comorbidities.
If you see an interesting Cohort Pathway you can copy and modify it. However, please avoid changing other researchers' Cohort Pathways.
In this example, we create a new cohort and select:
A Target Cohort defined by ICD10 asthma codes J45 and J46
An Event Cohort defined by the use of common asthma medicines
Both the Target and Event Cohorts must be defined before they can be used in Cohort Pathways.
Select the Cohort Pathways option from the left menu
Name the new Cohort Pathway using the text box at the top:
In this example, we have selected the J45_J46[MN]_Asthma Target Cohort:
In this example, we have selected four Event Cohorts that are displayed in following table:
Next, define the pathway analysis settings:
Collapse Days: the range of days for events to be assigned the earliest date in the range to reduce pathway variation during analysis.
Minimum cell count: the smallest number of individuals in the Target Cohort for the event to be included in the pathway.
If you wish to export results from the FinnGen Sandbox the number of reported individuals must be ≥ 5.
Maximum path length: the maximum of steps in a pathway in the Sunburst Plot.
Allow repeats: define if the same event (or event combination) is allowed to appear multiple times in the pathway.
Save the Cohort Pathway by clicking the Save button on the right side of the Cohort Pathway name:
Now we are ready to run the Pathway analysis.
Click the Executions tab.
Click the blue Generate button (shown after having been clicked below) for the FinnGen data release of your choice.
The red Cancel button is shown while the Pathway analysis is running.
Once the Pathway analysis is completed:
Click the All executions button and find your analysis run
Click the View reports link
People in the Target Cohort who are not in any of the Event Cohorts are excluded from the Pathway Analysis.
The results are visualized using a Sunburst Plot and can be downloaded in a tabular format by clicking the Tabular button.
The left panel shows Target Cohort details including the percentage of persons included in the Pathway Analysis. It also explains the Event Cohort (event) colors used in the Sunburst Plot.
The middle panel shows the Sunburst Plot with each circle in the plot describing one step in the Pathway Analysis. Different events are shown using different colors and in correct proportions. The innermost circle layer shows the people in the Target Cohort who are included in the first initial event. The second circle layer shows the second event in the pathway that happened after the first initial event. The third circle layer shows the third event, and so on. Two or more colors within a layer indicate simultaneous events. The order of the colors is fixed and does not indicate the chronological order of simultaneous events. The end of the pathway is indicated in grey.
The right panel shows details of a path after a point has been clicked in the Sunburst Plot.
Atlas documentation:
Click the button on the right
Click the Target Cohorts button to select the Target Cohort(s). A Target Cohort is the group of patients being investigated in the pathways of events.
Select your Target Cohort(s) from the provided list and click button at the bottom of the page. Use the Filter option to search for your cohort. Once you have selected the Target Cohort(s) they will appear in a table (see above).
Click the Event Cohorts button to select the Event Cohort(s) from the provided list. An Event Cohort defines the steps in this pathway and is usually defined using treatments, medicines, or comorbidities.
