Comments (6)
Hi Sophie, thanks for your interest in focus. My hunch is that rpy2 updated their interface. Can you tell me what version of rpy2 you're using? You can do this by opening a python terminal and typing
import rpy2
rpy2.__version__
from focus.
from focus.
from focus.
Finally, i didn't use focus script to convert the fusion weights to focus weight. I used RSQLite in R to construct the weights (.db) manually.
from focus.
Hi Sophie,
Sorry I couldn't reply sooner. It seems like you've managed to import the weights correctly using a workaround. I'm going to leave this open for now so I can implement a bugfix for the new rpy2 interface.
Thanks.
from focus.
I went back and tested this using rpy2 version 3.0.4 and was able to import weights. I'm wondering if this was related to the R installation itself. What version of R do you have installed?
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Related Issues (20)
- P less than 5e-8 but it says doesnt' exist HOT 7
- Importing weights from FUSION
- How to evaluate result of a gene in 2 region.
- Default --n-min in munge HOT 2
- FOCUS stalls on chromosome 6 HOT 3
- Importing weights from FUSION HOT 2
- Tissue prioritization HOT 1
- Cleaning GWAS summary data HOT 1
- Data folder doesn't contain gencode_map_v37.tsv HOT 8
- [ERROR] import_fusion 'Series' object has no attribute 'DIR' HOT 7
- unsupported operand type(s) for +: 'float' and 'str'
- [ERROR] Import submodule requires mygene and rpy2 to be installed
- [ERROR] ufunc 'isfinite' not supported for the input types HOT 2
- Please specify independent regions location or default regions with '37:EUR', etc HOT 2
- 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
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