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ctlab / LinSeed

Linseed: LINear Subspace identification for gene Expresion Deconvolution
MIT License
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How may we get deconvoluted matrix #9

Closed Sharks28 closed 4 years ago

Sharks28 commented 4 years ago

Is there a way to get final deconvoluted expression matrix? I am looking to extract expression for each cell type for each sample in the data. I want to import this deconvoluted matrix to the Seurat package and continue analysis.

konsolerr commented 4 years ago

Hi, @Sharks28

Sure, there is a way to do it, if your it is kept in slot "proportions" within your linseed object. Assume your linseed object called lo, then you can get the matrix as

lo$proportions

Cheers and sorry for the slow reply

Sharks28 commented 4 years ago

@konsolerr : thanks for getting back to me. Your solution would just give me matrix of proportions, right? I guess what I was going for is complete deconvolution matrix, where we can have expression of genes per cell type.

konsolerr commented 4 years ago

@Sharks28 Sorry, I somehow misread the question, this slot is called signatures

lo$signatures