Help
How to Use PRED-LD
PRED-LD is designed to facilitate GWAS summary statistics imputation using precalculated LD statistics. Follow these steps to get started:
- Upload Your Data: Begin by uploading a tab-separated text file containing SNP data via the 'Upload a Tab-Separated Text File' input in the sidebar. Please ensure your file follows the required format and does not exceed 20,000 rows.
- Configure Imputation Settings: Adjust the imputation settings to fit your needs. This includes selecting the LD resource, specifying the population, setting R² and MAF thresholds, and optionally providing a list of rsIDs for targeted imputation.
- You can also perform Imputation in specific rsIDs, after pressing the respective checkbox. You can upload them either as a .txt file or you can paste them.
- Execute Imputation: Click the 'Execute' button to start the imputation process. The application will process your data using the specified settings and display the results in the 'Imputation Results' tab.
- View and Download Results: Once the imputation is complete, you can view the LD Info and Imputation Results in their respective tabs. Use the download buttons provided to save the results to your device.
FAQs
Q: What file format should I use for my data?
A: Your input data should be in a tab-separated text file (TXT format). Ensure the file contains the necessary SNP information and adheres to the specified format.
Note: The A1 column represents the Alternative Allele (ALT), and the A2 column represents the Reference Allele (REF).
Q: How do I choose the right LD resource and population to perform Imputation?
A: The choice of LD resource and population should match the background of your study population. PRED-LD supports for the time three LD resources (Hap Map, Pheno Scanner and TOP-LD) and their respective populations. More specifically :
HapMap populations
Pheno Scanner and TOP-LD populations
Q: What does the R² threshold setting do?
A: The R² threshold determines the level of linkage disequilibrium (LD) required for SNPs to be considered in the imputation. A higher threshold will result in stricter LD filtering.
Q: Can I run another imputation with different settings without restarting the app?
A: Yes, you can adjust the settings as needed and click the 'Execute' button again to run another imputation. Use the 'Clear Screen' button to reset the app interface if needed.
Q: Where can I find more information about the populations and LD resources available in PRED-LD?
A: Detailed information about the populations and LD resources supported by PRED-LD can be found in the documentation provided on the PRED-LD GitHub page.
Need Further Assistance?
If you encounter issues or have questions not covered in this help section, please visit the PRED-LD GitHub page for more information or to contact to gmanios@uth.gr. Your feedback is valuable in improving PRED-LD.
About PRED-LD
PRED-LD
PRED-LD is a summary statistics imputation approach to enhance the resolution of genetic association studies. The method focuses on imputing summary statistics given beta coefficients and standard errors, using precalculated linkage disequilibrium (LD) statistics from HapMap, Pheno Scanner and TOP-LD. This approach provides a fast and accurate solution for imputing associations at untyped single nucleotide polymorphisms (SNPs) which are in high linkage disequilibrium. The presented method is also available as a standalone script.
PRED-LD GitHub repository:
https://github.com/pbagos/PRED-LD
LD resources:
HapMap
Pheno Scanner (data can be made available upon request)
TOP-LD
Contact Information:
Main Developer:
Georgios Manios (gmanios@uth.gr)
Also, vist :
Computational Genetics Group website
Your feedback is valuable in improving PRED-LD. For support or further information, please contact us via the provided links.