celdatosce {celda} | R Documentation |
SCE
objectConvert a old celda model object (celda_C
,
celda_G
, or celda_CG
object) to a
SingleCellExperiment object containing celda model
information in metadata
slot. Counts matrix is stored in the
"counts"
assay slot in assays
.
celdatosce( celdaModel, counts, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'celda_C' celdatosce( celdaModel, counts, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'celda_G' celdatosce( celdaModel, counts, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'celda_CG' celdatosce( celdaModel, counts, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'celdaList' celdatosce( celdaModel, counts, useAssay = "counts", altExpName = "featureSubset" )
celdaModel |
A |
counts |
A numeric matrix of counts used to generate
|
useAssay |
A string specifying the name of the assay slot to use. Default "counts". |
altExpName |
The name for the altExp slot to use. Default "featureSubset". |
A SingleCellExperiment object. Function
parameter settings are stored in the metadata
"celda_parameters"
slot.
Columns celda_sample_label
and celda_cell_cluster
in
colData contain sample labels and celda cell
population clusters. Column celda_feature_module
in
rowData contain feature modules.
data(celdaCMod, celdaCSim) sce <- celdatosce(celdaCMod, celdaCSim$counts) data(celdaGMod, celdaGSim) sce <- celdatosce(celdaGMod, celdaGSim$counts) data(celdaCGMod, celdaCGSim) sce <- celdatosce(celdaCGMod, celdaCGSim$counts) data(celdaCGGridSearchRes, celdaCGSim) sce <- celdatosce(celdaCGGridSearchRes, celdaCGSim$counts)