LoadingRNAFromSeurat

Load RNA data from a Seurat object, instead of RNAData from SampleInfo

Input

  • infile: An RDS or qs/qs2 format file containing a Seurat object.

Output

  • outfile: Default: {{in.infile | basename}}.

Environment Variables

  • prepared (flag): Default: False.
    Whether the Seurat object is well-prepared for the pipeline (so that SeuratPreparing process is not needed).
  • clustered (flag): Default: False.
    Whether the Seurat object is clustered, so that SeuratClustering (SeuratClusteringOfAllCells) process or SeuratMap2Ref is not needed.
    Force prepared to be True if this is True.
  • sample: Default: Sample.
    The column name in the metadata of the Seurat object that indicates the sample name.

SeeAlso