Cell metadata of the Sparse slot

cSparse() returns the cell metadata (colData) of the Sparse slot of a ScMaSigPro object; cSparse<- replaces it.

Usage

cSparse(object, value = "missing")

cSparse(object) <- value

# S4 method for class 'ScMaSigPro'
cSparse(object, value = "missing")

# S4 method for class 'ScMaSigPro'
cSparse(object) <- value

Arguments

object

A ScMaSigPro object.

value

A data frame with one row per cell, named after the cells of the Sparse slot and in their order, as cSparse() returns it. Without row names, the rows are taken in the order of the cells.

Value

cSparse(object): a data frame with one row per cell. cSparse<- and cSparse(object, value): the updated object, returned invisibly by the latter.

Details

The cells are the columns of the counts, and sc.squeeze() finds them by name, so a value with other cells or another order is an error. cSparse(object, value) sets value as cSparse(object) <- value does.

See also

Other accessors: cDense(), eDense(), eSparse(), pathAssign(), predictors()

Examples

data("scmp.ob", package = "scMaSigPro")
cells <- cSparse(scmp.ob)
head(cells[, c("Pseudotime", "Path")])
#>       Pseudotime  Path
#> Cell1         42 Path2
#> Cell2         41 Path1
#> Cell3         23 Path1
#> Cell4         42 Path1
#> Cell5         79 Path2
#> Cell6          1 Path1

# Add a column to the cell metadata
cells$early <- cells$Pseudotime < 50
cSparse(scmp.ob) <- cells