Manage Sample Clinical Data

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Contents

Manage Sample Clinical Data

Overview

Users with sufficient Land privileges can manage columns of "Clinical Data" to samples.

For example, columns can be added, updated, or removed, and Clinical Data can be organized/grouped to be better organized in the Filter window.

To access this function, click Manage | Samples | Manage Sample Clinical Data:

Land ManageClinicalData Menu.png

Options

Land ManageClinicalData Window.png

Add Clinical Data

Clinical data columns can quickly be added for one or more samples.

The input table should have Sample IDs (matching Land Sample IDs) in the first column. Additional columns can contain data (groupings, sample characteristics, etc).

Clicking Add Clinical Data will bring up the following window:

Land AddClinicalData Window.png

The source table for clinical data can be loaded from:

  • tab-delimited file: A text table, with data in a row separated by tabs
  • .osobj file: An OmicSoft Table object from an Analysis project, saved as an osobj file.
  • local analysis: An OmicSoft Table object from an Analysis project.
  • triplets: A tab-delimited file for sparse data, where column 1 is sample ID, column 2 is variable name, and column 3 is the value. See an example here.
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Add Clinical Variable Metadata

Remove Selected Samples

To remove ALL clinical data for selected samples, first select those samples in the table, then click Remove Selected Samples.

You will see the warning

Land RemoveSelectedSamples Window.png

Click Yes to permanently remove the clinical data for those selected samples.

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Remove Selected Clinical Variables

To remove selected clinical data for ALL samples, first select those clinical data, then click Remove Selected Clinical Variables.

You will see the warning

Land RemoveSelectedClinicalVariables Window.png

Click Yes to permanently remove the selected clinical data for all samples.

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Related Articles

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