Comments (1)
quattro
commented on August 17, 2024
I'm considering just dropping this feature for now. Looking at the code there are still some bugs, and the current implementation can't be distributed/parallelized in an easy way for the FOCUS db. Given typical datasets will have 1000s of models to train it would be painfully slow to use any reasonable penalized model.
I think the easier approach would be to use FUSION or PrediXcan to train en masse, and then import after-the-fact.
from focus.
Related Issues (20)
- Integer column has NA values in column 3 HOT 4
- unsupported operand type(s) for +: 'float' and 'str' HOT 3
- Focus import error - "500 Server Error: Internal Server Error for url: http://mygene.info/v3/query/" HOT 2
- ERROR] MetaData.__init__() got multiple values for argument 'schema' HOT 1
- error in creating the weight database HOT 3
- symbol issue when creating weight database using Predixcan databases HOT 5
- name 'zscores' is not defined errror with when running finemap with --intercept HOT 2
- The TWAS z-score obtained by S-PrediXcan and FOCUS software is different
- [WARNING] Unable to match ENSG00000228327.3 to Ensembl ID. Using ID for symbol HOT 2
- The --prior-prob parameter set for DNA methylation based fine-mapping analysis
- p-values in the output plot is on negative natural log scale? HOT 2
- Some example files/databases unavailable
- data for re-plotting the expression correlation as in the plot output
- "block" issue on FOCUS HOT 3
- focus finemap error HOT 6
- [error] dataframe.pivot() takes 1 positional argument but 4 were given HOT 7
- Modifying the focus.db
- Error when perform finemap for splicing-based association study
- ERROR] pivot() takes 1 positional argument but 4 were given
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from focus.