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mortazavilab / PyWGCNA

PyWGCNA is a Python package designed to do Weighted Gene Correlation Network analysis (WGCNA)
https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btad415/7218311
MIT License
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WGCNA and GeneExp class documentation does not match parameter names #69

Closed ofarrelle closed 6 months ago

ofarrelle commented 8 months ago

https://github.com/mortazavilab/PyWGCNA/blob/5ffb26682d389e5eb288e0762b58bf268b2c3065/PyWGCNA/wgcna.py#L79 https://github.com/mortazavilab/PyWGCNA/blob/5ffb26682d389e5eb288e0762b58bf268b2c3065/PyWGCNA/geneExp.py#L21

In both classes, the parameter for the gene expression matrix is called 'geneExp', but documentation calls it 'geneExpr' This tripped me up briefly so I thought posterity might find updating this helpful.

Thanks for providing this package!

nargesr commented 7 months ago

Hello,

Sorry for the confusion! The naming might be a little bit difficult to understand at first. In nutshell, the geneExpr is an object from geneExp class while geneExp is an expression matrix. In the documentation, I try to include all the attributes as well as initial input.

Please let me know if the current version is still confusing.