Pseudo-bulk counts of the Dense slot

eDense() returns an assay of the Dense slot of a ScMaSigPro object, genes by bins, as a dense matrix; eDense<- sets one.

Usage

eDense(object, i = "bulk.counts", ...)

eDense(object, i = "bulk.counts") <- value

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

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

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

Arguments

object

A ScMaSigPro object.

i

The name of the assay. With the default, "bulk.counts", eDense() 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 bin of the Dense slot. Its row and column names, when present, must be the gene and bin names of the slot in the same order; missing names are filled in.

Value

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

Details

eDense<- 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(), eSparse(), pathAssign(), predictors()

Examples

data("scmp.ob", package = "scMaSigPro")
bulk <- eDense(scmp.ob)
bulk[1:3, 1:4]
#>       Path1_bin_1 Path1_bin_2 Path1_bin_3 Path1_bin_4
#> Gene1          16          24          11          31
#> Gene2        6335        7337        3375        9161
#> Gene3         201         245         105         216

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