SlingshotDataSet {slingshot} | R Documentation |
This is a convenience function to extract a
SlingshotDataSet
from an object containing slingshot
output. However, we now recommend using a
PseudotimeOrdering
object, in most cases.
The SlingshotDataSet
is, however, still used for plotting purposes.
SlingshotDataSet(data, ...) ## S4 method for signature 'SingleCellExperiment' SlingshotDataSet(data) ## S4 method for signature 'SlingshotDataSet' SlingshotDataSet(data) ## S4 method for signature 'PseudotimeOrdering' SlingshotDataSet(data)
data |
an object containing |
... |
additional arguments to pass to object-specific methods. |
A SlingshotDataSet
object containing the output of
slingshot
.
PseudotimeOrdering
,
as.SlingshotDataSet
data("slingshotExample") rd <- slingshotExample$rd cl <- slingshotExample$cl library(SingleCellExperiment) u <- matrix(rpois(140*50, 5), nrow = 50) sce <- SingleCellExperiment(assays = list(counts = u), reducedDims = SimpleList(PCA = rd), colData = data.frame(clus = cl)) sce <- slingshot(sce, clusterLabels = 'clus', reducedDim = 'PCA') SlingshotDataSet(sce)