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neurogenomics / MAGMA_Celltyping

Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Add functions to find intersection of genes with high genetic load + cell type specificity (similar to approach used in Parkinsons nature genetics paper) #40

Closed williamlam314 closed 2 years ago

williamlam314 commented 3 years ago

Dear Nathan,

Thank you for sharing your code. I am an iBSC student at UCL and have been using this pipeline to identify association between different liver disease and cell types and have got some interesting data. I was wondering whether it would be possible to obtain the intersection of genes between the gwas sum stats and the cell type data, in essence the genes driving the association?

NathanSkene commented 3 years ago

In principle you can get it by looking at the scores associated with each gene in the MAGMA file. I've never found an approach for doing this that I consider particularly meaningful though.

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Dear Nathan,

Thank you for sharing your code. I am an iBSC student at UCL and have been using this pipeline to identify association between different liver disease and cell types and have got some interesting data. I was wondering whether it would be possible to obtain the intersection of genes between the gwas sum stats and the cell type data, in essence the genes driving the association?

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williamlam314 commented 3 years ago

Dear Nathan,

Thank you for your response. I was wondering if you might have an idea therefore on how, having identified a cell type significantly associated with disease, one should then prioritise targets to investigate for functional relevance in that cell type?

bschilder commented 2 years ago

Hi @williamlam314 this is now implemented in the function MAGMA.Celltyping::get_driver_genes. Hope it answers your questions!