Importing weights from FUSION

[huanhuanzhu0212]

Hi,

I am trying to import FUSION weights to focus. The FUSION weights are directly downloaded from FUSION databases (http://gusevlab.org/projects/fusion/).

The directory test/ contains two files:
~/test$ ls
Minor_Salivary_Gland Minor_Salivary_Gland.P01.pos

"Minor_Salivary_Gland" is a directory containing all .wgt.RDat weight files. Minor_Salivary_Gland.P01.pos is a file with weight lists: Minor_Salivary_Gland/*****.wgt.RDat.

Under directory test/, I run:
focus import Minor_Salivary_Gland.P01.pos fusion --tissue Minor_Salivary_Gland --name GTEx --assay rnaseq --output DB_NAME

There is always an error:

Starting log...
[2019-07-10 12:30:56 - INFO] Preparing weight database
[2019-07-10 12:30:57 - ERROR] 'rpy2.rinterface.SexpEnvironment' object has no attribute 'find'
[2019-07-10 12:30:57 - INFO] Finished importing prediction models

I also tried to import weights from PrediXcan and it works, so FOCUS should be successfully installed and can be used. Then, i think it might be due to FUSION weights, but the weights are directly downloaded and all the packages needed for FUSION and focus are installed.

Any suggestions will be appreciated. Thank you for your help!
Sincerely,
Sophie

[quattro]

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__

[huanhuanzhu0212]

Dear Dr. Mancuso, Thank you so much for your reply! The rpy2 version is 3.0.4. [image: image.png] Sincerely, Sophie

…

On Wed, Jul 10, 2019 at 1:30 PM Nicholas Mancuso ***@***.***> wrote: 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__ — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#13?email_source=notifications&email_token=AJ3E5SKPGYKYVZVBLZ5ZC6DP6YMEBA5CNFSM4H7RGQK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUFXRY#issuecomment-510155719>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AJ3E5SPTIJ3LB4A6FXXEU23P6YMEBANCNFSM4H7RGQKQ> .

[huanhuanzhu0212]

Dear Dr. Mancuso, If this error is due to new rpy2 interface and it is not easy to deal with. I will try to convert the FUSION .RDat weights into FOCUS .db format manually. Would you mind telling me that which components ("model","modelattribute", "molecularfeature" ,"refpanel", "weight") are actually being used in further FOCUS fine mapping analysis. Besides "weights", which component is useful, i will try to construct it. Also, could you briefly tell me the matches between FUSION .RDat and FOCUS .db? It will hugely help me to convert. Thank you very much for your time! Sophie

…

On Wed, Jul 10, 2019 at 1:43 PM Sophie Zhu ***@***.***> wrote: Dear Dr. Mancuso, Thank you so much for your reply! The rpy2 version is 3.0.4. [image: image.png] Sincerely, Sophie On Wed, Jul 10, 2019 at 1:30 PM Nicholas Mancuso ***@***.***> wrote: > 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__ > > — > You are receiving this because you authored the thread. > Reply to this email directly, view it on GitHub > <#13?email_source=notifications&email_token=AJ3E5SKPGYKYVZVBLZ5ZC6DP6YMEBA5CNFSM4H7RGQK2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGODZUFXRY#issuecomment-510155719>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AJ3E5SPTIJ3LB4A6FXXEU23P6YMEBANCNFSM4H7RGQKQ> > . >

[huanhuanzhu0212]

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.

[quattro]

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.

[quattro]

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?