Issue with Monocle3 Compatibility

[Sophya Yeoh]

Hi,

I am currently working on using Cicero and wanted to use Monocle3 according to the example protocol. After making the input_cds with the make_atac_cds function, I can't pass the input_cds through the Monocle3 functions. I keep getting this error message:

Error: methods::is(object = cds, class2 = "cell_data_set") is not TRUE

Is there a way to work around this?

Best wishes,

Sophya

[hpl...@gmail.com]

Hi, sorry for the delay. Can you please check the class of the input_cds that you're passing through? For example running class(input_cds) 

[Flávia Gan]

Hello, everyone!!

I'm having the same problem!
Did you manage to figure out how to fix it? When I check the created object, this message returns:
"CellDataSet (storageMode: environment)
assayData: 33762072 features, 68889 samples
   element names: exprs
protocolData: none
phenoData
   sampleNames: AAACTACCAGAAACCCGAGATA AAACTACCAGAAACCTAAGTGG ... TTCCATCCTCTTTGCCGGAAGG (68889
     total)....."

However, when I go to the later stages of the analysis, the same error as yours returns.

[hpl...@gmail.com]

Hello,

Looks like you've loaded a monocle object rather than a monocle3 object. Make sure that you haven't loaded the monocle library and load your data using one the options shown here: https://cole-trapnell-lab.github.io/monocle3/docs/getting_started/#loading-data . The created object should be of type cell_data_set rather than CellDataSet. Hope that helps!

Best,

Hannah