Cell counts of the Sparse slot

eSparse() returns an assay of the Sparse slot of a ScMaSigPro object, genes by cells, as a dense matrix; eSparse<- sets one.

Usage

eSparse(object, i = "counts", ...)

eSparse(object, i = "counts") <- value

# S4 method for class 'ScMaSigPro'
eSparse(object, i = "counts", ...)

# S4 method for class 'ScMaSigPro,character'
eSparse(object, i = "counts") <- value

# S4 method for class 'ScMaSigPro,missing'
eSparse(object, i = "counts") <- value

Arguments

object

A ScMaSigPro object.

i

The name of the assay. With the default, "counts", eSparse() returns the first assay when no assay has that name.

...

Not used.

value

A matrix, a dgCMatrix or a data frame of numbers, with one row per gene and one column per cell of the Sparse slot. Its row and column names, when present, must be the gene and cell names of the slot in the same order; missing names are filled in.

Value

eSparse(): a numeric matrix. eSparse<-: the updated object.

Details

eSparse<- stores value as a dgCMatrix. It gives a message when it creates a new assay and a warning when it replaces one.

See also

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

Examples

data("scmp.ob", package = "scMaSigPro")
counts <- eSparse(scmp.ob)
counts[1:3, 1:4]
#>       Cell1 Cell2 Cell3 Cell4
#> Gene1     0     2     1     2
#> Gene2   436   371   432   427
#> Gene3    35    13    17    18

# Add a second assay
eSparse(scmp.ob, "logcounts") <- log1p(counts)
#> Creating a new assay as 'logcounts'.