Closed lxwang326 closed 3 years ago
exp_mtx
needs to be set prior to the function call. How to do so is generally described here: https://python-textbok.readthedocs.io/en/1.0/Variables_and_Scope.html.
Right, you will need to read in the expression matrix before running this function. You can use something like
from pyscenic.cli.utils import load_exp_matrix
exp_mtx = load_exp_matrix("expr_mat.csv")
when run
%time auc_mtx = aucell(exp_mtx, regulons, num_workers=32) auc_mtx.to_csv(AUCELL_MTX_FNAME)
error
CPU times: user 13 µs, sys: 1 µs, total: 14 µs Wall time: 26.2 µs
NameError Traceback (most recent call last) /tmp/ipykernel_33904/2692781098.py in
1 get_ipython().run_line_magic('time', '')
----> 2 auc_mtx = aucell(exp_mtx, regulons, num_workers=32)
3 auc_mtx.to_csv(AUCELL_MTX_FNAME)
NameError: name 'exp_mtx' is not defined
any help?