Comments (1)
Hi Yuanzhe,
It looks like a bug from a rare case that we failed to pay attention to in our tests. Thanks for pointing it out and we will get it fixed ASAP.
Currently, I can share you some work around for this issue:
# You can include as many other datasets to use here
peakDatasets <- c("atac")
# Extract `ligerDataset` class objects requested
datasetObjList <- datasets(int.bmmc)[peakDatasets]
# Extract the peak matrices
# Make sure these datasets are of "atac" modality so it has the slots, otherwise it'll show you an error
rawPeakList <- lapply(datasetObjList, slot, "rawPeak")
peakLiger <- createLiger(rawPeakList)
peakLiger <- normalize(peakLiger)
# Transfer the cluster labels from the original object to the new temporary object for marker calling
peakLiger$cluster <- cellMeta(int.bmmc, "leiden_cluster", useDatasets = "atac")
defaultCluster(peakLiger) <- "cluster"
# It should work this time to run marker detection now
markerTable <- runMarkerDEG(peakLiger)
Hope this works for you! Please feel free to reach out if there's still any issues.
Best,
Yichen
from liger.
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