scater (version 1.0.4)

fromCellDataSet: Convert a CellDataSet to an SCESet

Description

Convert a CellDataSet to an SCESet

Usage

fromCellDataSet(cds, exprs_values = "tpm", logged = FALSE)

Arguments

cds

A CellDataSet from the monocle package

exprs_values

What should exprs(cds) be mapped to in the SCESet? Should be one of "exprs", "tpm", "fpkm", "counts"

logged

logical, if a value is supplied for the exprsData argument, are the expression values already on the log2 scale, or not?

Value

An object of class SCESet

Examples

data("sc_example_counts")
data("sc_example_cell_info")
pd <- new("AnnotatedDataFrame", data = sc_example_cell_info)
example_sceset <- newSCESet(countData = sc_example_counts, phenoData = pd)
if ( requireNamespace("monocle") ) {
    # cds <- toCellDataSet(example_sceset) # not run
    # sceset <- fromCellDataSet(cds) # not run
}