Extract Monocle2 "State" for Seurat
Hello,
I am currently running Monocle2 and have generated a trajectory plot with three different "states", is it possible to extract this state information to input as a column of data in the Seurat metadata, so that I can run FindMarkers?
Thank you in advance for helping write this code.
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fracarb8
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written
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cgp09741 •
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written
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cgp09741 •
1 answer
You need to check how monocle 2 stores data inside the celldata set. To save the pseudotime from monocle 3 (not 2) to seruat I usually do:
seuratObject <- AddMetaData(
object = seuratObject,
metadata = monocleObject@principal_graph_aux@listData$UMAP$pseudotime,
col.name = paste0("Pseudotime_",condition)
)
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