8 Adding Meta data
Whether you created a new Seurat object or you resumed processing a Seurat object, the first step will be to add Meta data. Meta data information for a Seurat object refers to information about the experiment or sample which was used to generate the data. This information can be used to compare different samples or identify the cells within an integrated Seurat object.
Meta data can be added to a Seurat object by clicking the Add time point/treatment information button.
Select the category from the drop down menu and type in the value for that field.
For example: Select the Time Point category if you wish to enter the time point at which the sample was collected. Enter the sample time point information (for ex. 48h) in the text box and click add. This will add 48h to the Time Point category in the meta data information of Seurat object.
After you select the category the actual value might be slightly different. This is necessary to prevent space or any other special characters impact analysis downstream.
8.1 Individual category of meta data and the actual value added to the Seurat object
- Time Point –> TimePoint
- Developmental stage –> DevStage
- Treatment –> Treatment
- Sample –> Sample
- Age –> Age
- Gender –> Gender
- Replicate –> Replicate
- ID –> IDvalue
8.2 Add meta data from a file
Sometime the metadata information for all the cells might be available. In this case, a .csv or .txt file can be used to upload the data.
The meta data file should contain the cell names or the barcode information as the row ID and the meta data value as the column name.
| barcode/meta_data | Cell.type | Sample | TimePoint | … |
|---|---|---|---|---|
| AATGGTCTATTCGGAT-1 | Vascular | early | 1 | … |
| AATTTACCATTCTTAC-1 | Vascular | early | 2 | … |
| GGTCTACCATTCTTAC-1 | Valve | late | 1 | … |
| … | … | … | … | … |
- You can add meta data from such a file using the Load Meta data from file. The use the Browse.. to locate the file.
In the process of addition of the meta data, the Seurat object will be subset to include only cells (barcodes) that are available in the meta data file.
8.3 Load meta data from column name
In cases where the data carries the meta data information embedded in the column names, you can use the use Use cell names to get Meta information.
This is useful when loading data sets where the gene counts information from 10x integrated/aggregated data. During integration/aggregation, library ID information in the form of -1 or -2 and so on, is added to the barcode corresponding to the individual samples from the sample_sheet
Other instances where the data information such as source of the cells or treatment might have been added to column names. These can be parsed using this approach.
When you are resuming the processing of a Seurat object you can choose to skip Adding meta data by clicking on the Next step!