association.Seurat: Extract information from Seurat object to create CNA object
In korsunskylab/rcna: Covarying Neighborhood Analysis

View source: R/utils_Seurat.R

association.Seurat

R Documentation

Extract information from Seurat object to create CNA object

Description

Extract information from Seurat object to create CNA object

Usage

association.Seurat(
  seurat_object,
  test_var,
  samplem_key,
  graph_use,
  batches = NULL,
  covs = NULL,
  nsteps = NULL,
  verbose = TRUE,
  assay = NULL,
  key = "NAMPC_"
)

Arguments

`seurat_object`	Initialized Seurat object. Assumes that FindNeighborhoods has been run.
`test_var`	Contrast variable to test for association.
`samplem_key`	String denoting the name of the sample-level identifier (e.g. DonorID).
`graph_use`	Which graph to use. By default, will use first graph in seurat_object.
`batches`	Name of batch variable. Currently only one categorical variable allowed.
`covs`	Name(s) of other (numerical) covariates to control for.
`nsteps`	TBD
`verbose`	TBD
`assay`	Which seurat assay to save results under.
`key`	Which key to use for cached NAM PC dimensions.