Closed sinarueeger closed 5 years ago
Hi @maousi,
For the sake of a Pull Request I made three tiny changes to your Jupyter Notebooks.
Here is a good paper on GWAS QC and the thresholds you can use: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/pdf/MPR-27-na.pdf
The viral PC's look a bit strange. Here are my first two PCs for comparison. I am using logisticPCA and a different imputation. Still weird that it looks so different.
Hi @maousi,
For the sake of a Pull Request I made three tiny changes to your Jupyter Notebooks.
Here is a good paper on GWAS QC and the thresholds you can use: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6001694/pdf/MPR-27-na.pdf
The viral PC's look a bit strange. Here are my first two PCs for comparison. I am using logisticPCA and a different imputation. Still weird that it looks so different.