The zip file file located in this directory is contains a set of R datafiles containing the specificity data used to calculate schizophrenia cell type enrichments in our 2017 paper "Genetic Identification Of Brain Cell Types Underlying Schizophrenia". Generation of this specificity data is described in the methods section of that paper.
The files are in an Rdata formatted designed to be used with the EWCE and MAGMA.Celltyping packages available from: https://github.com/NathanSkene
After load the file into R, the level 1 annotation specificity values can be viewed as:
So if you want the specificity of Parvalbumin in Interneurons then type:
Alternatively, to see the mean level of expression (in terms of Unique Molecular Identifiers) then type:
If you want to get the equivilent values for level 2 annotations then instead type:
If you use these datasets please cite our paper:
"Genetic Identification Of Brain Cell Types Underlying Schizophrenia", Nature Genetics, May 2018, Nathan G. Skene, Julien Bryois, Trygve E. Bakken, Gerome Breen, James J. Crowley, Helena Gaspar, Paola Giusti-Rodriguez, Rebecca D. Hodge, Jeremy A. Miller, Ana Munoz-Manchado, Michael C. O'Donovan, Michael J. Owen, Antonio F. Pardinas, Jesper Ryge, James T. R. Walters, Sten Linnarsson, Ed S. Lein, Patrick F. Sullivan, Jens Hjerling-Leffler