as.PseudotimeOrdering {slingshot} | R Documentation |
This function converts objects that contain slingshot
results into a PseudotimeOrdering
.
as.PseudotimeOrdering(x, ...) ## S4 method for signature 'SlingshotDataSet' as.PseudotimeOrdering(x) ## S4 method for signature 'SingleCellExperiment' as.PseudotimeOrdering(x) ## S4 method for signature 'PseudotimeOrdering' as.PseudotimeOrdering(x)
x |
an object containing |
... |
additional arguments to pass to object-specific methods. |
A PseudotimeOrdering
object containing the slingshot
results from the original object, x
.
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') as.PseudotimeOrdering(sce)