Notes for the application of PrediXcan to neuropsychiatric phenotypes.
This folder contains the scripts and notes used to generate the figures in the manuscript: "Transcriptome association studies of neuropsychiatric traits in African Americans implicates PRMT7 in schizophrenia"
GWAS and PrediXcan summary statistics can be found within this folder. These data include both p-values and lsfr results for PrediXcan associations.
This folder contains the scripts used to generate plots for the manuscript. Scripts to generate plots following revisions can be found within the Reviews folder.
This folder contains scripts used for the QC, Imputation, GWAS, PrediXcan, and adaptive shrinkage. The scripts in this folder are refered to within the markdown documents.
Files in this folder contain introductory notes regarding the QC, Imputation, GWAS, and PrediXcan application on the GAIN dataset only.
Files in this folder contain notes regarding the QC, Imputation, GWAS, and Predixcan application to all of the African American individual data from the Molecular Genetics of Schizophrenia study. (Accession Numbers: phs000021.v2.p1 (GAIN) and phs000167.v1.p1 (nonGAIN) ) Additional notes that can be found in this folder contain the comparison of gene imputation reference panels for GTEx V6 and GTEx V7.
Files in this folder contain the notes regarding the QC, Imputation, GWAS, and Predixcan application to all of the African American individual data from the GAIN bipolar disorder dataset (Accession: phs000017.v3.p1). Considering the similarity of methods used to compare gene imputation panels in reference to phenotypic association, some imputation panel comparisons may be found in MGS_SCZ as well.