add_cor_scores could only selects capitalized genes?
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Description
Hi Kai,
While I was running add_cor_scores for some mouse data, I found that the select argument could only take capitalized gene names. I used
network = snap.tl.init_network_from_annotation(regions,
anno_file = snap.genome.mm10,
upstream=500000,
downstream=500000,
id_type='gene_name',
coding_gene_only=True)
to set up the network. As I ran
snap.tl.add_cor_scores(network,
gene_mat = expr,
peak_mat = damage,
select = variable_gene,
overwrite = True) only one gene would get selected. Adding var_upper = [gene.upper() for gene in variable_gene]
would pass all the genes I wanted to the add_cor_scores function. Thanks for the help in advance!
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Research direction
Start by reproducing the issue with snap.tl.init_network_from_annotation and snap.tl.add_cor_scores using the mouse mm10 network and a lowercase gene list. Trace how the select argument is matched against gene names, then verify that lowercase names select the intended genes without requiring callers to uppercase them.
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Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100