TensorQTL analysis problem

[Juyeol-Jung]

TensorQTL analysis problem

[francois-a]

Hi,
TensorQTL uses the qvalue package from R to estimate FDR. For this to be run, R needs to be installed with this package, together with rpy2 for Python. This is then called here, and adds the qval column to the dataframe.

[Juyeol-Jung]

Thank you for your kindness reply.

Because of other work, I check your reply now and I try running tensorQTL.

[abiddanda54gene]

Hello @francois-a, I am running into a similar issue where I need the qval column for --mode cis_independent. I am not able to find rfunc for python and am unsure of how to get it. Could you please advise?

[francois-a]

rfunc is part of tensorQTL, and contains a wrapper for qvalue. You'll need R and rpy2, as described above.

[jonathonl]

I'm having the same issue as @abiddanda54gene. Both R and rpy2 are installed, but rfunc is failing to import.

$ python3 -c "import subprocess; print(subprocess.call('which R', shell=True, stdout=subprocess.DEVNULL, stderr=subprocess.DEVNULL)); import rpy2; import tensorqtl"
0
Warning: 'rfunc' cannot be imported. R and the 'rpy2' Python package are needed.

[jonathonl]

The issue is that Iterable as been removed from collections in python v3.10 (see https://stackoverflow.com/questions/72032032/importerror-cannot-import-name-iterable-from-collections-in-python). Modifying line 5 of rfunc.py to be from collections.abc import Iterable fixes the import error.

[francois-a]

Hi, thanks for pointing this out. Fixed in eb72058.