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atarashansky / SAMap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.
MIT License
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Harmony integration (was closed issue #83) #131

Closed dsb66 closed 11 months ago

dsb66 commented 11 months ago

I am running the current version of SAMap (v1.0.15). I am trying to use the batch option with the command sm.run(batch_key="batch") but I get the error: TypeError: run() got an unexpected keyword argument 'batch_key'.

Has the batch_key option been removed from the current version?

atarashansky commented 11 months ago

SAMap never had a batch_key. Perhaps you're thinking of SAM?

dsb66 commented 11 months ago

I see - I am sorry this the first time I work with SAMap/SAM. So the procedure would be: 1- normalize and log-transform individual datasets 2- concatenate datasets, separately for each species 3- integrate concatenated objects in SAM 4- run SAMap Is this correct? Thanks!

atarashansky commented 11 months ago

Do you have AnnData objects with raw counts? What's your input data look like? What's your objective?

SAM is a method to analyze individual datasets. SAMap is a method that integrates SAM objects together across species.

dsb66 commented 11 months ago

I have 4 human and 4 mouse datasets (raw counts). I want to integrate the datasets from each species, before running SAMap to integrate the human and mouse integrated objects. What would be the correct sequence of steps?

atarashansky commented 11 months ago

Concatenate all human data into one AnnData, load it into SAM, then run SAM with batch_key set to your batch key. Do the same for mouse. Then you need to pass them into SAMap. At this stage, please refer to the SAMAP tutorial notebook in this repo.

dsb66 commented 11 months ago

Great - thank you very much!