Up: Component summary
Up: Component summary
Component
FCSReaderFCSReader imports a FCS file (standards 2.0 and 3.0 supported) and converts it into a tab-delimitted CSV file.
| Version | 1.0 |
|---|---|
| Bundle | flowand |
| Categories | FlowCytometry |
| Authors | Julia Casado (julia.casado@helsinki.fI), Ville Rantanen (ville.rantanen@helsinki.fI) |
| Requires | libnlopt-dev (DEB) ; R ; flowCore (R-bioconductor) |
| Source files | component.xml FCSReader.r |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| in | Array<FCS> | Mandatory | Array of FCS files |
| annotations | CSV | Optional | Contains channel names correspondence with cell markers, such as primary or secondary antibodies. |
Outputs| Name | Type | Description |
|---|---|---|
| out | Array<CSV> | Array of CSV files. Columns represent different variables measured in the experiment, for instance time, scatters and channels. Rows represent individual cells. Channel values are compensated using the spillover matrix in the FCS-files if parameter compensate is true. |
| metadata | CSV | CSV file containing the "Key" from the array and some information from the header of the corresponding FCS file. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| compensate | boolean | false | If true, the data is compensated using the spillover matrix in each FCS file. |