getReferenceSingleCellRNA: getReferenceSingleCellRNA

In UMMS-Biocore/dprofiler: Dprofiler:

getReferenceSingleCellRNA

Description

Prepares Seurat objects for Compositional Profiling

Usage

getReferenceSingleCellRNA(
  object,
  name,
  marker_ident = NULL,
  subsetProp = NULL,
  subset_seed = 1,
  subset_ident = NULL,
  subset_ident_min = 10,
  subset_assay = "RNA",
  subset_data = "counts",
  subset_embedding = "tsne"
)

Arguments

object	Seurat Object
name	name of the Single Cell Reference
marker_ident	Ident of Seurat Object for marker analysis
subsetProp	Proportion of single cell data to downsize, if NULL the entire single cell data is used
subset_seed	The seed for random sampling
subset_ident	Ident to subset the single cell data, if NULL cells are randomly selected
subset_ident_min	Minimum number of cells in an ident, ignored if subset_ident is NULL
subset_assay	Seurat assay used in the subset
subset_data	Seurat data used in the subset
subset_embedding	Seurat embedding used in the subset

Examples

# library
library(Seurat)

# prepare scRNA reference data
referencePBMC <- getReferenceSingleCellRNA(pbmc_small)
                                           
# prepare scRNA reference data, select idents for markers analysis and subsetting                                          
referencePBMC <- getReferenceSingleCellRNA(pbmc_small, marker_ident = c("RNA_snn_res.0.8","RNA_snn_res.1"), 
                                           subsetProp = 0.8, subset_ident = "RNA_snn_res.0.8", subset_ident_min = 10)

UMMS-Biocore/dprofiler documentation built on Oct. 16, 2022, 11:37 a.m.