RunCoGAPS: Run CoGAPs on a Seurat object

In satijalab/seurat-wrappers: Community-Provided Methods and Extensions for the Seurat Object

Run CoGAPs on a Seurat object

Description

Run CoGAPs on a Seurat object

Usage

RunCoGAPS(
  object,
  assay = NULL,
  slot = "counts",
  params = NULL,
  temp.file = NULL,
  reduction.name = "CoGAPS",
  reduction.key = "CoGAPS_",
  ...
)

Arguments

object	Seurat object
assay	Assay to pull data from
slot	Slot to pull data from.
params	CogapsParams object for specifying parameter settings
temp.file	Name of temporary data matrix file to create if running in a distributed mode. Setting to TRUE will generate the file name using tempfile.
reduction.name	Name of the CoGAPS reduction returned
reduction.key	Key for the CoGAPS reduction returned

Value

Returns a Seurat object with the CoGAPS results stored as a DimReduc object

References

E.J. Fertig, J. Ding, A.V. Favorov, G. Parmigiani, and M.F. Ochs (2010) CoGAPS: an integrated R/C++ package to identify overlapping patterns of activation of biological processes from expression data. Bioinformatics 26:2792-2793.

See Also

CoGAPS

satijalab/seurat-wrappers documentation built on April 10, 2024, 3:25 p.m.