Al-Murphy
commented
2 years ago Hey!
To go from GWAS SNPs to instigated cell types have a look at MAGMA celltyping which was also developed in our lab. This package uses EWCE once it relates SNPs to genes. Have a look at the documentation and vignettes there and you will find what you're looking for. Unfortunately you will need to plot the heatplot yourself as it isn't a standard output but the data is all there.
Cheers, Alan.
Is your feature request related to a problem? Please describe. Is there any way to extract this proportional expression gene matrix, and plot?
Describe the solution you'd like I want a function that can calculate the proportional expression across an annotation level, for each of the genes in the hits.
Describe alternatives you've considered A clear and concise description of any alternative solutions or features you've considered.
Additional context I was reading this paper https://www.nature.com/articles/s41586-021-04369-3, and in Figure 6A, they were able to plot this as a heatmap, as shown.
In their figure legend, it describes "Proportional expression of the top 45 AD GWAS genes across all major brain cell types. Expression values for a given gene sums to 1 across cell types using the EWCE method. Genes ordered in approximate risk strength39–41,51. Asterisks denote the strongest expressing cell types."
I am thinking about doing similar things, if you have this feature implemented.
Thanks!