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Import the seurat project into monocle or monocle3 for pseudotime analysis #469

Open cli35 opened 3 years ago

cli35 commented 3 years ago

Dear All, I am stressed with doing pseudotime analysis. I had performed scaling and dimensionality reduction on the filter_matirx data. I would like to further process the pseudotime analysis with one cluster I created before in the seurat. However, I have problem import the seurate project into monocle. I imported the data like below, but an error appeared

cds.c1.cattle <- newCellDataSet(as(as.matrix(seurate.c1.10x@assays$RNA@data), 'sparseMatrix'), phenoData = seurate.c1.10x@meta.data, featureData = gene_annotation.c1) Error: CellDataSet 'phenoData' is class 'data.frame' but should be or extend 'AnnotatedDataFrame'

brgew commented 3 years ago

Hi,

Have you seen the documentation on the Seurat WWW site?

https://htmlpreview.github.io/?https://github.com/satijalab/seurat-wrappers/blob/master/docs/monocle3.html