Seurat v3 input matrices for monocle

[s849]

Hi,

I was wondering if anyone has tried to use Monocle2 using input matrices derived from Seurat v3? I was able to do it before (with Seurat v2), but now I am not sure if I am doing it correctly. Using the following input information, I was able to get Monocle2 to work:

expr_matrix <- subset@assays$integrated[,names(subset@active.ident)]
sample_sheet = data.frame(row.names=colnames(expr_matrix),cluster=subset@active.ident, genotype=subset@meta.data$orig.ident)
gene_annotation <- data.frame(row.names=rownames(expr_matrix), gene_short_name=rownames(expr_matrix))

## create a new CellDataSet object
pd <- new("AnnotatedDataFrame", data = sample_sheet) 
fd <- new("AnnotatedDataFrame", data = gene_annotation) 
newData <- newCellDataSet(as(as.matrix(expr_matrix), "sparseMatrix"),phenoData = pd,featureData = fd,lowerDetectionLimit=0.5,expressionFamily=negbinomial.size())

Thanks!

[andrewwbutler]

Hi,

We don't currently have an conversion function in v3 for Monocle but Monocle2 has a function here to import v2 Seurat objects. You can check your code against that to ensure everything is going to the right place.

[timoast]

Hi, we are in the process of adding Seurat -> Monocle conversion and it will be available soon (see #1241)

[HomairaH]

Is the v3 -> Monocole conversion available?

[Sophia409]

@mojaveazure Same question,Is the v3 -> Monocole conversion available?
Recently monocle 3 has upgraded.And after I modify the code that is used to import seurat object according to new new_cell_data_set function,it gave errors. Can you give me some help?Thank you very much.

#262 how to import seurat object
data <- Merge.integrated@assays$RNA@data
cell_metadata <- new('AnnotatedDataFrame', data = Merge.integrated@meta.data)
fData <- data.frame(gene_short_name = row.names(data), row.names = row.names(data))
gene_metadata <- new('AnnotatedDataFrame', data = fData)
#Construct monocle cds
tdcds <- new_cell_data_set(data,
cell_metadata = cell_metadata,
gene_metadata = gene_metadata
)`

Error in as.data.frame.default(from) : cannot coerce class ‘structure("AnnotatedDataFrame", package = "Biobase")’ to a data.frame