selectFeatures | 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)
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