MetabolicExprImputation

This process imputes the dropout values in scRNA-seq data.

It takes the Seurat object as input and outputs the Seurat object with imputed expression data.

You can turn off the imputation by setting the noimpute option of the process group to True.

Input

  • infile: The input file in RDS/qs format of Seurat object

Output

  • outfile: Default: {{in.infile | stem}}.imputed.qs.
    The output file in RDS format of Seurat object Note that with rmagic and alra, the original default assay will be renamed to RAW and the imputed RNA assay will be renamed to RNA and set as default assay.

Environment Variables

  • tool (choice): Default: alra.
    Either alra, scimpute or rmagic
    • alra: Use RunALRA() from Seurat
    • scimpute: Use scImpute() from scimpute
    • rmagic: Use magic() from Rmagic
  • scimpute_args (ns): The arguments for scimpute
    • drop_thre (type=float): Default: 0.5.
      The dropout threshold
    • kcluster (type=int): Number of clusters to use
    • ncores (type=int): Default: 1.
      Number of cores to use
    • refgene: Default: "".
      The reference gene file
  • rmagic_args (ns): The arguments for rmagic
    • python: Default: python.
      The python path where magic-impute is installed.
    • threshold (type=float): Default: 0.5.
      The threshold for magic imputation.
      Only the genes with dropout rates greater than this threshold (No. of cells with non-zero expression / total number of cells) will be imputed.
  • alra_args (type=json): Default: {}.
    The arguments for RunALRA()

Reference