Closed Juyeol-Jung closed 2 months ago
francois-a
commented
2 years ago 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
commented
2 years ago Thank you for your kindness reply.
Because of other work, I check your reply now and I try running tensorQTL.
abiddanda54gene
commented
2 years ago 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
commented
2 years ago rfunc is part of tensorQTL, and contains a wrapper for qvalue. You'll need R and rpy2, as described above.
jonathonl
commented
1 year ago 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.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
commented
1 year ago Hi, thanks for pointing this out. Fixed in eb72058c776ecd473a9bef7afe88ad4385edc5e4.
Hi, I'm user for analyzing sc-eQTL by using tensorQTL. Thanks for developing great tool to understand SNP's role for bioscience.
I've got problem to analyse sc-eQTL by tensorQTL's cis_independent mode. Based on error information, It is occurred by pandas-based q-value estimation but I cannot easily access this problem.
These are running process result during tensorQTL's running process.
[Jul 19 17:09:24] Running TensorQTL: cis-QTL mapping
To avoid creating the large chunks, set the option
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/site-packages/tensorqtl-1.0.5-py3.9.egg/tensorqtl/main.py", line 2, in
tensorqtl.main()
File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/site-packages/tensorqtl-1.0.5-py3.9.egg/tensorqtl/tensorqtl.py", line 144, in main
res_df = cis.map_independent(genotype_df, variant_df, summary_df, phenotype_df, phenotype_pos_df, covariates_df,
File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/site-packages/tensorqtl-1.0.5-py3.9.egg/tensorqtl/cis.py", line 653, in map_independent
signif_df = cis_df[cis_df[fdr_col]<=fdr].copy()
File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/site-packages/pandas/core/frame.py", line 3505, in getitem
indexer = self.columns.get_loc(key)
File "/ess/discovery/users/juyeol/99.tools/python/lib/python3.9/site-packages/pandas/core/indexes/base.py", line 3623, in get_loc
raise KeyError(key) from err
KeyError: 'qval'
I hope this information is worth for contributing this problem's solution.
and can you give some information for rfunc's role in this analysis??
Thank you.