VariableSet

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Variable Set

Definition

A variable set is a set of metadata columns saved under a common name. The Variable Set can be loaded when filtering the Sample Distribution, Clinical Table data, Sample Details and many other views where the option “Specify Columns” is available.

VariableSets are available for both Genetics and Disease lands.

The variable set is not tied to a user and can be used by anyone having access to the land.


If a variable set has only empty categories and they are not dynamic columns, the variable set needs to be updated to also display the column categories and be able to be used properly.

Example of VariableSet with empty categories:

VarSet emptyCategories.jpg

Example of VariableSet with correct categories:

VarSet withCategories.jpg

Creating a variable set

Via the menu

The first way of creating a variable set is by entering the Menu Manage -> Variable Sets -> Manage Variable Sets

ManageVarSetMenu.jpg

Here, just like in the case of Sample or Gene Sets, by pressing the add button, a new window will be displayed, where you can enter the variable set details. VarSet AddButton.jpg

AddVarSet Window.jpg

The Variable Set can be saved only when a variable set name and at least one column is selected. Right after clicking ok, the variable set will be available in the menu and can be used in other analysis.

Via the Choose Columns window

The second way of creating a variable set is by going to the “Choose columns” window and then clicking on “Save VariableSet”, like below:

Alternate AddVarSet.jpg

In this case, only the name of the variable set must be specified, as the columns will be read directly from the “Choose columns” window.

Updating a variable set

A variable set can be updated only by entering the Menu Manage -> Variable Sets -> Manage Variable Sets and clicking the edit button. VarSet EditButton.jpg

The same window will be opened like in Creating a Variable Set via the menu. The same restrictions apply as well: a variable set can be saved only with a valid name and at least one column.

Deleting a variable set

The variable set can only be deleted from the Manage Variable Set menu, by clicking on the delete button.


A confirmation window will be displayed to confirm the deletion of the variable set:

Delete VarSet.jpg

After the deletion, the list of variable sets for that land will be updated automatically. The deletion of a variable set is not reversible and will affect all users.

Loading a variable Set

To load a variable set, open the “Choose Columns” window in any view like Sample Distribution, Clinical Table data, Sample Details, etc, click the “Load VariableSet” button, choose the variable set you are interested in and finally click “Ok”.

VarSet Load.jpg

The list of columns will be automatically filtered based on the selected columns.

Variable set examples

Example 1: Searching for EGR1

When searching on 1000G land for gene “egr1” the default SNP view will display all 92 columns. If one is interested just in the columns “egr1” and “usubjID”, one would have to remove all columns, search manually for the columns “egr1” and “usubjID” and then reload the view.

By loading a previously saved variable set with “egr1” and “usubjID”, we no longer need to search for these columns.

CodingMatrix WithoutVarSet.jpg

After selecting the variable set in image … and then clicking ok in the “Choose Column” window, the column list will be filtered like below:

CodingMatrix WithVarSet.jpg