diff --git a/README.md b/README.md index 875ff9e..5890ed6 100644 --- a/README.md +++ b/README.md @@ -20,11 +20,11 @@ Our reference datasets consisted of summary statistics from previously published * Latino GWAS meta-analysis; Loesch et al 2021; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Loesch2021_Parkinsons_HS) • Alzheimer's disease - - AD GWAS meta-analysis; Bellenguez et al 2022; https://www.ebi.ac.uk/gwas/ (accession no. GCST90027158) - * FinnGen Release 6; [see here](https://r6.finngen.fi/pheno/G6_AD_WIDE_EXMORE) - * African American GWAS meta-analysis; Kunkle 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33074286) - * East Asian GWAS meta-analysis; Shigemizu et al 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33654092) - * Latino GWAS meta-analysis; Lake et al 2023; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Lake2023_AD_Mixed) + * AD GWAS meta-analysis; Bellenguez et al 2022; https://www.ebi.ac.uk/gwas/ (accession no. GCST90027158) + * European AD GWAS meta-analysis; [see here](https://dss.niagads.org/datasets/ng00075/) + * African American GWAS meta-analysis; Kunkle 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33074286) + * East Asian GWAS meta-analysis; Shigemizu et al 2021; [see here](https://www.ebi.ac.uk/gwas/publications/33654092) + * Latino GWAS meta-analysis; Lake et al 2023; [see here](https://ndkp.hugeamp.org/dinspector.html?dataset=Lake2023_AD_Mixed) ### Helpful Links - *coming soon* pre-print @@ -44,7 +44,7 @@ Our reference datasets consisted of summary statistics from previously published ├── analyses │   ├── 00_clean_and_prep_PD.ipynb │   ├── 01_PAR_calculations_PD.ipynb -│   ├── 02_clean_and_prep_AD.ipynb +│   ├── 02_clean_and_prep_AD_revised.ipynb │   ├── 03_PAR_calculations_AD.ipynb │   ├── 04_PD_EUR_fine_mapping.ipynb │   ├── 05_PD_AFR_fine_mapping.ipynb @@ -69,7 +69,7 @@ Our reference datasets consisted of summary statistics from previously published |:-----------------------------:|:------------------------------------------------------------------------------------------------------------------------------------------------:| | 00_clean_and_prep_PD.ipynb | Load list of 90 PD risk loci from Nalls publication, import ancestry-specific GWAS summary statistics, select top hits, and identify known/population-specific variants for analysis. | | 01_PAR_calculations_PD.ipynb | Calculate population attributable risk (PAR) for each target and generate a table with summary statistics and PAR. | -| 02_clean_and_prep_AD.ipynb | Import AD datasets for each ancestry, clean and filter p-values < 0.05, select top hits for each ancestry, and generate dataset for calculations. | +| 02_clean_and_prep_AD_revised.ipynb | Import AD datasets for each ancestry, clean and filter p-values < 0.05, select top hits for each ancestry, and generate dataset for calculations. | | 03_PAR_calculations_AD.ipynb | Calculate population attributable risk (PAR) for each target and generate a table with summary statistics and PAR. | | 04_PD_EUR_fine_mapping.ipynb | Extract chromosome and base pair positions from summary statistics for selected loci in EUR population, perform fine-mapping, and save results. | | 05_PD_AFR_fine_mapping.ipynb | Extract chromosome and base pair positions from summary statistics for selected loci in AFR population, perform fine-mapping, and save results. |