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satijalab / seurat

R toolkit for single cell genomics
http://www.satijalab.org/seurat
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Adding MAGIC to Seurat #585

Closed scottgigante closed 6 years ago

scottgigante commented 6 years ago

Hi,

We spoke a while ago about adding PHATE and eventually MAGIC to Seurat. MAGIC has just been submitted to CRAN and is in a stable state.

How should a tool such as MAGIC interact with Seurat? Do you currently have any imputation methods included in the package that I can use to model the API?

Thanks, Scott

mschilli87 commented 6 years ago

Another case that ~would~could benefit from https://github.com/satijalab/seurat/issues/586.

satijalab commented 6 years ago

Agreed! We don't have an API that works well with this yet, but will in the future- and will keep you updated as things progress.

huqingtao2018 commented 6 years ago

@scottgigante Hi, scott,

After running MAGIC, I want to use the result dataframe as input for RunMultiCCA in Seurat package. I don't know which slot should the MAGIC dataframe be put (raw.data, data or scaled.data?), I put the MAGIC result at data slot and got error message when running RunMultiCCA(something like subscription out of bound). Is this caused by those negtive value in the MAGIC dataframe? Woud you please give any suggestion on it?

Thank you. Best wishes!

scottgigante commented 6 years ago

@huqingtao2018 , how one would insert external data into an existing object is not my expertise - you're better off opening a separate issue to discuss this. MAGIC returns a data.frame with one column for every row, in which missing values are imputed; you might be best off creating a new Seurat object for this, but as I said, the Seurat help manual or authors are better positioned to answer your question.

mschilli87 commented 6 years ago

@scottgigante: @huqingtao2018 opened https://github.com/satijalab/seurat/issues/612 for this.