VariableSet

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A Variable Set is a saved set of columns (e.g. Sample Metadata, Clinical Data, Association Metadata, etc).

Contents

Variable Set details

The Variable Set is saved per Land and shared across all users of the Land.
It can be used to load a set of columns frequently used in an analysis, to save the set of columns for later use, or to simplify a view with a lot of columns.
The Variable Set is integrated in the following views:

  • Land context : Sample Distribution, Association Distribution, Histogram of Variables, Numeric Variable Summarizations, Table View, Clinical Table View
  • GeneticsLand Variant context : Variant.SnpGenotypes, Variant.VcfSnpGenotypes, Variant.CovariateVariableView, Variant.VcfSnpMatrix, Variant.AssociationTable
  • GeneticsLand Variant Set context : VariantSet.VcfSnpMatrix, VariantSet.CodingMatrix, VariantSet.AssociationTable
  • GeneticsLand Gene context : Gene.VcfSnpMatrix, Gene.VcfSnp.CarrierSampleDetails, Gene.VcfSnp.CodingMatrix, Gene.AssociationTable
  • GeneticsLand Gene Set context : GeneSet.VcfSnpMatrix, GeneSet.VcfSnp.CodingMatrix, GeneSet.AssociationTable
  • GeneticsLand Region context : Region.VcfSnpMatrix, Region.VcfSnp.CarrierSampleDetails, Region.VcfSnp.CodingMatrix, Region.AssociationTable
  • GeneticsLand Association context : Association.TopHits
  • GeneticsLand Association Set context : AssociationSet.TopHits

Opening the variable sets

There are 2 places where you can view or manage the Variable Sets.

Specify columns

This menu is available on the right side of the Land view, under the Task Tab. In the picture below it's marked with 1. After the Specify Columns dialog is opened, the user can either choose to load one of the existing Variable Sets or save the current list of columns as a new Variable Set.
To load a Variable Set, simply select a set from the pop-up dialog and click Ok. The associated list of columns will be displayed in the 'Selected Column' list.
To save a Variable Set, after selecting the list of columns, press the Save VariableSet link and enter the new VariableSet name. The variable set will immediately be available to all users connected on the server.

VariableSet - Menu 1.png

Manage Variable Sets

To edit, delete, or create a new Variable Set use the new Manage Variable Set menu. The menu is similar to Manage Sample Set in ArrayLand menu.
ManageVariableSet.png

In the Manage Variable Set screen, one can use the Add, Edit or Delete buttons to make changes to the Variable Sets.
After the Add or Edit buttons are pressed, the below dialog will open, where the user can add or edit the columns.
UpdateVariableSet.png

Important notes

Saving a Variable Set

When adding or editing a Variable Set from the Manage Variable Set screen, the user can only save the Variable Set if the name and selected columns are not empty.

Loading a Variable Set

When a Variable Set is loaded in a different context than the one it was created it in, it will load all found columns. This means, that in the worst case scenario, no columns will be loaded and all initial columns will be moved back to the Available columns list.

Related Articles

ArrayLand Download dialogs also include the variable set option, which allows users to specify a collection of columns from metadata which will be downloaded.

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