cDense() returns the bin metadata (colData) of the Dense slot of a
ScMaSigPro object, one row per pseudotime bin; cDense<-
replaces it.
Usage
cDense(object, value = "missing")
cDense(object) <- value
# S4 method for class 'ScMaSigPro'
cDense(object, value = "missing")
# S4 method for class 'ScMaSigPro'
cDense(object) <- valueArguments
- object
A ScMaSigPro object.
- value
A data frame of bin metadata, one row per bin.
Value
cDense(object): a data frame with one row per bin. cDense<-
and cDense(object, value): the updated object, returned invisibly by the
latter.
Details
The bins are the columns of the pseudo-bulk counts. A value with one
row per bin replaces the metadata and keeps the counts; its rows may be
renamed, and pb_counts() then recomputes the counts. A value with
another number of rows, such as bins rebuilt by hand, cannot keep the
counts: the Dense slot then holds the metadata without counts, a
message says so, and pb_counts() must be run before the next step.
cDense(object, value) sets value as cDense(object) <- value does.
See also
Other accessors:
cSparse(),
eDense(),
eSparse(),
pathAssign(),
predictors()
Examples
data("scmp.ob", package = "scMaSigPro")
bins <- cDense(scmp.ob)
head(bins[, c("Path", "scmp_binned_pseudotime", "scmp_bin_size")])
#> Path scmp_binned_pseudotime scmp_bin_size
#> Path1_bin_1 Path1 1 14
#> Path1_bin_2 Path1 2 15
#> Path1_bin_3 Path1 3 7
#> Path1_bin_4 Path1 4 17
#> Path1_bin_5 Path1 5 13
#> Path1_bin_6 Path1 6 11
# Add a column to the bin metadata
bins$early <- bins$scmp_binned_pseudotime <= 4
cDense(scmp.ob) <- bins