selectFeatures {celda} | R Documentation |
A simple heuristic feature selection procedure.
Select features with at least minCount
counts
in at least minCell
cells. A SingleCellExperiment
object with subset features will be stored in the
altExp slot with name altExpName
.
The name of the assay
slot in altExp
will be the same as useAssay
.
selectFeatures( x, minCount = 3, minCell = 3, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'SingleCellExperiment' selectFeatures( x, minCount = 3, minCell = 3, useAssay = "counts", altExpName = "featureSubset" ) ## S4 method for signature 'matrix' selectFeatures( x, minCount = 3, minCell = 3, useAssay = "counts", altExpName = "featureSubset" )
x |
A numeric matrix of counts or a
SingleCellExperiment
with the matrix located in the assay slot under |
minCount |
Minimum number of counts required for feature selection. |
minCell |
Minimum number of cells required for feature selection. |
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 with a
altExpName
altExp slot. Function
parameter settings are stored in the metadata
"select_features"
slot.
data(sceCeldaCG) sce <- selectFeatures(sceCeldaCG) data(celdaCGSim) sce <- selectFeatures(celdaCGSim$counts)