RunGLMPCA: Run GLMPCA

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

Run GLMPCA

Description

Run GLMPCA

Usage

RunGLMPCA(
  object,
  L = 5,
  assay = NULL,
  features = NULL,
  reduction.name = "glmpca",
  reduction.key = "GLMPC_",
  verbose = TRUE,
  ...
)

Arguments

object	A Seurat object
L	The number of dimensions to return (defaults to 5)
assay	Assay to use, defaults to the default assay
features	A list of features to use when performing GLM-PCA. If null, defaults to variable features.
reduction.name	Name to store resulting DimReduc object as. Defaults to glmpca
reduction.key	Key for resulting DimReduc. Defaults to GLMPC_
...	Extra parameters passed to glmpca

Value

A Seurat object containing the output of GLMPCA stored as a DimReduc object.

Author(s)

Will Townes

References

Townes, W., Hicks, SC, Aryee, MJ, Irizarry, RA. (2019). "Feature selection and dimension reduction for single-cell RNA-Seq based on a multinomial model." Genome Biology.

Examples

## Not run: 
pbmc_small
pbmc_small <- RunGLMPCA(pbmc_small)
DimPlot(pbmc_small, redunction = 'glmpca')

## End(Not run)

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