README.md

How to run MAGMA

(1) Prepare summary statistics

Because summary statistics are not uniformly released, preparation differs per summary statistics.

prepare_MAGMA_sumstats.sh

(2) (optional) Sensitivity analyses (HapMap3 restriction and MHC exclusion)

QC_MAGMA.sh

(3) Run MAGMA Top 10% mode and Linear mode using 10x Genomics and KI level 1 scRNA data

MAGMA_v.1.08_celltype_analysis_hm3_mhc_restricted.R

(4) Run MAGMA Top 10% mode and Linear mode using KI level 2 scRNA data

MAGMA_v.1.08_celltype_analysis_hm3_mhc_restricted_KI_level2_v33.R

(5) (optional) Run sensitivity analyses in schizophrenia

MAGMA_v108_celltype_analysis_SCZ_all_QC.R

Reference files

To map rsids for SNPs without CHRPOS, 1kg .bim files were used.

Reference data used for MAGMA analyses can be found here.

Also see the original MAGMA Celltyping repository

Skene, et al. Genetic identification of brain cell types underlying schizophrenia. Nature Genetics, 2018.