add_cor_scores
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- Python
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Description
Hi,
I ran into error when running
net = snap.tl.init_network_from_annotation(regions,
anno_file =snap.genome.hg38,
upstream = 250000,
downstream= 250000,
id_type = 'gene_name',
coding_gene_only = True)
net = snap.tl.add_cor_scores(net, gene_mat=gene_mat, peak_mat=peak_mat, select=None, overwrite=False)
error shows:
net = snap.tl.add_cor_scores(net, gene_mat=gene_mat, peak_mat=peak_mat, select=None, overwrite=False)
if sp.issparse(y):
y = y.todense()
scores = np.ravel(spearman(X.T, y.reshape((1, -1))))
for nd, sc in zip(nd_X, scores):
setattr(network.get_edge_data(nd, nd_y), key, sc)
Looking forward to your reply!
Thanks
tingting
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Research direction
Start by reproducing the failure with the init_network_from_annotation setup and the snap.tl.add_cor_scores call shown, capturing the complete traceback. Done means the cause is identified and the call succeeds, or the failure is narrowed to a reproducible case with a verified fix.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100