SeuObj_transfer: SeuObj_transfer

In yuanqingyan/singleGEO: Query and Analysis of High-throughput Single Cell Sequencing Data from GEO

SeuObj_transfer

Description

Transfer reference data information onto query data.

Usage

SeuObj_transfer(
  RefObj = RefObj,
  QueryObj = QueryObj,
  RefLabel = RefLabel,
  Norm.method = "lognorm",
  Future.globals.maxSize = 12000 * 1024^2
)

Arguments

RefObj	A reference Seurat object. Required.
QueryObj	The query Seurat object. Required.
RefLabel	The column name of meta data from RefObj. This label will transfer to query data. Required.
Norm.method	Normalization method. The standard LogNormalize or sctransform. Options of: "lognorm" or "sct". Default: "lognorm"
Future.globals.maxSize	Maximum allowed total size of global variables. Default: 12000*1024^2 (12Gb)

Value

The Seurat object of query data with predicted labels from reference data.

Examples

library(singleGEO)
###

data(Data_Ref_transfer)
data(Data_Query_transfer)

Transfer_Result<-SeuObj_transfer(RefObj=Data_Ref_transfer,
                                QueryObj=Data_Query_transfer,
                                 RefLabel="defined")
Seurat::DimPlot(Transfer_Result,
                group.by="predicted.RefLabel",
                reduction = "umap",
                label=TRUE,
                repel = TRUE)+ NoLegend()

yuanqingyan/singleGEO documentation built on Jan. 11, 2025, 6:35 p.m.