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FCSReader

FCSReader 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.

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