Closed rahilgholami closed 1 year ago
Yes, this isn't ideal really... There's currently no argument for this. However: The cluster
function defaults to using the "exprs"
assay. So you could rename the assay you'd like to use to this, and run the clustering. I.e.,
i <- match("exprs_normalized", assayNames(sce))
assayNames(sce)[i] <- "exprs"
sce <- cluster(sce, ...)
Hi,
I would like to pass the assay type (e.g.
assay.type = “exprs_normalized”
) to thecluster(spe, features = rownames(spe), maxK = 30, seed = 220410)
function but it doesn't know the argument. Is there any way to set the assay type? My data are read in as a SpatialExperiment object.I would be grateful for any help.
Best, Rahil