Multiple ways to add sampleset in Land

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SampleSets in Land

A SampleSet in OmicSoft Lands is simply a list of interesting samples, but it optionally can have additional metadata columns, such as mutation status, tissue type, or essentially anything else you might find useful. A SampleSet can be created by selection or filters, by Land analytics, or imported from a user-created text file. SampleSets are stored on-server and can be shared via subscription.

Create/Group SampleSet from Selection/Filter

Once the user has a subset of sample of interest, the user could create or group sampleset from selection/filter from the Action tab:

SampleSet1.png

Create Sample Set From Selection/Filter will create a sample set only with the sample of the user's selection; while Group Sample Set From Selection/Filter will create a sample set of all samples with an annotation column indicating whether a sample is of the user's selection:

Sampleset2.png


In the Upload SampleSet window, type in the Name and Tag, the Metadata tab will automatically load your sample of selection:

Sampleset3.png

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Create Sample Set From Selection/Filter:

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Creating sample set will only contain the sample ID of the user's selection.

Group Sample Set From Selection/Filter:

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Grouping sample set will included all samples but with an additional annotation column indication whether the sample is selected or not. This could be used to compare the selected and unselected samples in downstream analysis.

Generate Sampleset from Land Analytics

To generate sampleset from Land Analytics, let's take generating Gene Mutation Status Sample Set as an example:

Sampleset7.png

For details, please refer to Generate Gene Mutation Status Sample Set

Add sampleset from Online meta data

Except creating sample set, sample set can also be generated from online metadata. Please refer to Manage SampleSet in ArrayLand: Add From Online for detailed instruction

Load sampleset from text files

The user could also upload sample set by uploading text files:

Go to Manage Sample Sets:

Sampleset8.png

In the Manage Sample Sets window, Add Sampleset:

Sampleset9.png

In the Metadata tab, upload your pre-created txt file with a list of gene name through Load from tab delimited file:

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Use sampleset for new land queries

Customized sampleset can be used to customize grouping, filtering and land data downloading. The user could easily use the sampleset information to compare samples and visualize samples in preferred way.

Grouping:

Sampleset12.png

Filtering:

Sampleset13.png

Land data download:

Sampleset14.png