Extract Monocle2 "State" for Seurat

Question

[cgp09741]

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.

Answer 1

[fracarb8]

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)
)