Add code to generate tile plots for a set of GWAS, with num genome-wide signif loci displayed above, with neat X-axis labels, using IEUGWAS to import details for the labels

[montenegrina]

Hello,

Can you please point me to the code from your repository which you use to create Fig 2b in your paper "Genetic identification of brain cell types underlying schizophrenia "

Thanks
Ana

[NathanSkene]

[bschilder]

Original issue name: tile plot 2B from the paper

@NathanSkene is this the magma.tileplot function?

Not sure if you have additional code for the LDSC half of the plot (which would be outside of MAGMA.Celltyping which only deals with MAGMA to my knowledge).

New issue name: Add code to generate tile plots for a set of GWAS, with num genome-wide signif loci displayed above, with neat X-axis labels, using IEUGWAS to import details for the labels

I can work on something like you've described using OpenGWAS..

[NathanSkene]

I've never managed to get the LDSC code packaged up. Have always wanted to get an LDSC.celltyping package setup. Will try and find a masters student to take it on.

[bschilder]

GenomicSEM actually has R wrappers for LDSC and S-LDSC.

Here's their wiki page for S-LDSC.