fromCellDataSet: Convert a 'CellDataSet' to an 'SCESet'

In dynverse/scaterlegacy: Single-cell analysis toolkit for gene expression data in R

Description

Convert a CellDataSet to an SCESet

Usage

fromCellDataSet(cds, exprs_values = "tpm", logged = FALSE,
  logExprsOffset = 1)

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 exprs_values="exprs", are the expression values already on the log2 scale, or not?
logExprsOffset	numeric, value to add prior to log-transformation.

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
}

dynverse/scaterlegacy documentation built on Feb. 17, 2020, 5:07 a.m.