Perform Shannon Component Analysis on a Seurat object — RunSCA • pochi

Perform Shannon Component Analysis on a Seurat object

Usage

RunSCA(
  object,
  assay = "RNA",
  slot = "data",
  n.comps = 50L,
  iters = 3L,
  reduction.name = "sca",
  reduction.key = "sca_"
)

Arguments

object: Seurat object
assay: Which assay to use for SCA calculation
slot: Which slot in the assay to use for SCA calculation
n.comps: Number of SCs to calculate
iters: How many iterations to perform for SCA
reduction.name: Name of the Reduction object to store the SCA as
reduction.key: Key preceding the numbers of SCA components in reduction.name

Value

Returns a Seurat object with an SCA calculated

References

Demeo and Berger, _biorxiv_ 2021. shannonca.readthedocs.io