How to make survival plots variant omic data querys in Geneticsland

From Array Suite Wiki

Jump to: navigation, search

GeneticsLand Survival Data View

The survival data view is available for GeneticsLands that have survival metadata (SurvivalTimeColumn, SurvivalStatusColumn, SurvivalDeathStatus) in their sample metadata. This view plots a Kaplain-meier curve with the option to apply a log-rank test.



Customizing This View

  1. Basic properties of the plot and the survival curve lines can be changed using the options Change Chart Properties and Change Line Properties under the Task tab.
  2. In the Task tab options users can also select to Show Summary Information and display a P-value.
  3. If the user has imported Sample Sets containing additional metadata columns that are compatible with survival data, users can set the metadata columns for Time, Status, Event, and Strata using Specify the Survival Columns.
  4. The survival view can be customized by applying Filters using the Query Control. For example, the user can filter for a specific tumor or clinical meta data parameter. The plot will dynamically update to chart the per-subject survival data, split by recalculated quartiles.

Make Variant Data Query

For detailed instructions on how to perform variant-level data queries please visit Add GeneticsLand Custom Query. After the query has been performed, it should be visible as a Custom Query in the Query Control.

Re-set the Grouping to the custom query (red arrow) to apply the sample categorization to the survival data plot. Users can further re-fine groupings by using the Task Tab options. Users can trellis by a covariate and as an example, explore the association of Project ID groupings with survival.

Note that individuals with missing meta data will automatically be excluded from the view; however, you must manually 'uncheck' the individuals with missing data for your variant of interest (ie. ./.)