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.
    Multiple columns will be concatenated with _ to form the sample name.
  • mutaters (type=json): Default: {}.
    The mutaters to mutate the metadata Keys are the names of the mutaters and values are the R expressions passed by dplyr::mutate() to mutate the metadata.
  • subset: An expression to subset the cells, will be passed to dplyr::filter().
    This will be applied after mutating the metadata.
  • ncores (type=int): Default: 1.
    The number of threads used to load/save the Seurat object.

SeeAlso

Description

Loads the RNA data from a pre-existing Seurat object (an RDS or qs/qs2 file) instead of the RNAData directories listed by SampleInfo. This is not a wrapper of an upstream analysis tool: the process is immunopipe's own and runs an R script that ships with immunopipe (immunopipe/scripts/LoadingRNAFromSeurat.R), which reads and writes the object with tidyseurat and qs2.

Base class

biopipen.core.proc.Proc - biopipen's bare process class, which declares no parameters of its own.

Deviations

All six options of this process are added by immunopipe, since the base class declares none: prepared (default False), clustered (default False), sample (default Sample), mutaters (default {}), subset (default None) and ncores (default 1).