Example: Visualizing Genotype Browser output data with TVT

With Genotype Browser you can select individuals based on a genotype you may be interested in and by importing them to the Trajectory Visualization Tool (TVT) you can investigate the medical history of the individuals as a group of people.

Step 1.

Follow the Steps 1-3 in this example to download the data you want from Genotype Browser.

Step 2.

In order to examine the medical history of people with TVT, it is important to create Concept Sets that include the medical codes you want to visualize. These instructions can help you with defining the Concept Set. You can visualize up to six Concept Sets at a time with TVT.

Step 3.

Open TVT from Applications. From Data sources, select the appropriate Data source. Click Browse... from Cohort as FINNGENIDs file and open the .tsv file you have downloaded from Genotype Browser.

Step 4.

After opening the file from Genotype Browser in TVT, open the Encoding section. Into the Concept set, type the name of the Concept Set you made in Atlas. Equip or unequip the Non-standard option according to if your Concept Set codes are non-standard codes or not. After you are finished, press Extract. If you have more than one Concept Set to visualize, you can select every Concept Set into different blocks and press Extract all. For detailed instructions, see Running TVT.

Now you are ready to inspect the medical codes within the Concept Set(s) with the help of Viewing TVT results.