Converts Seurat object to Expression Set
'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.
SeuratToExpressionSet(
seurat.object,
delimiter,
position,
version = c("v2", "v3")
)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. |
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.
sc.eset Expression set containing relevant phenotype and individual data, cellType and SubjectName.
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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.