SeuratToExpressionSet: Converts Seurat object to Expression Set

In cozygene/bisque: Decomposition of Bulk Expression with Single-Cell Sequencing

Description

'SeuratToExpressionSet()' returns an Expression Set with phenotype data indicating cell type (cellType) and individual (SubjectName) for each cell in a Seurat object. Raw counts data is used for assay data.

Usage

SeuratToExpressionSet(
  seurat.object,
  delimiter,
  position,
  version = c("v2", "v3")
)

Arguments

seurat.object	Seurat object with attributes raw.data, ident, and cell.names
delimiter	Character to split cell names with to find individual ID.
position	Integer indicating 1-indexed position of individual ID after splitting cell name with delimiter.
version	Character string. Either "v2" or "v3. Seurat version used to create Seurat object.

Details

Note that the Seurat and Biobase libraries should be attached before running this function. The delimiter and position arguments are used to infer the individual ID from the cell ID. For example, a delimiter of "-" and position of "2" indicates that the individual ID for the cell ID ACTG-2 would be 2.

Value

sc.eset Expression set containing relevant phenotype and individual data, cellType and SubjectName.

Examples

  library(Seurat)
  library(Biobase)

  # We make a class to emulate a Seurat v2 object for illustration only
  setClass("testSeuratv2", representation(cell.names = "character",
                                          ident = "character",
                                          raw.data = "matrix"))
  sc.counts <- matrix(0,nrow=3,ncol=3)
  # These barcodes correspond to a delimiter of "-" and position 2 for individual id.
  test.cell.names <- c("ATCG-1", "TAGC-2", "GTCA-3")
  test.ident <- c("cell type a", "cell type b", "cell type c")
  names(test.ident) <- test.cell.names
  colnames(sc.counts) <- test.cell.names
  test.seurat.obj <- new("testSeuratv2",
                         cell.names=test.cell.names,
                         ident=test.ident,
                         raw.data=sc.counts)

  single.cell.expression.set <- SeuratToExpressionSet(test.seurat.obj, delimiter='-',
                                                      position=2, version="v2")

cozygene/bisque documentation built on May 28, 2021, 7:57 p.m.