Comments (7)
Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?
from focus.
Hi, I also have the same issues that I have empty log file say that there is not p<5e-8. Not sure if anyone response to @Captain-Pam ? Was this issue resolve?
There has been no solution to this problem. If you are interested, can we try to solve it together?
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I am interested to work together. I also have empty log file. I notice that the p<5e-8 is a warning and wasn't an error. I also tried using lower threshold and does not work. It is frustrating and I cannot move forward using it. I also email the creator, but has not heard back from him.
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Hi @Captain-Pam, I think I may have a reason. I need to use the focus.db rather than gtex_v7.db https://www.dropbox.com/s/ep3dzlqnp7p8e5j/focus.db?dl=0
Try and see if it works for you after switching to focus.db. It is working for me now. I am not sure why gtex_v7.db not working for me.
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Apologies for delayed response. Seeing this thread now. A few things:
- I plan to replace the v7 db with an updated v8 soon.
- Can you manually output regions that contain p < 5e-8 and contrast those with the pre-defined LD blocks from LDetect? It may be that some loci are dropped.
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Hi @sookwah-yee @quattro. it is strange, seeing the example, it used the gtex_v7.db. However, I downed GTEx v8.db from PredictDB website (mashr model) to created the focus.db file by using ‘FOCUS import‘ command. So I agree with @quattro , maybe the locus is not in the LD block from LDetect.
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Hi @Captain-Pam and @quattro, thank you for sharing the information for what you did.
I would like to try using GTEx v8.db soon and I wonder which one did you use @Captain-Pam ? There are four different one under Mashr model. Also if I use the v8.db and do the focus.import, do I need to convert the RSID to the different format?
mashr_eqtl.tar: PrediXcan’s and S-PrediXcan’s support on expression
mashr_sqtl.tar: PrediXcan’s and S-PrediXcan’s support on splicing
gtex_v8_expression_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan expression’s LD reference
gtex_v8_splicing_mashr_snp_smultixcan_covariance.txt.gz: S-MultiXcan splicing’s LD reference
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Related Issues (20)
- 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
- 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
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