nargesr
commented
9 months ago Hi,
Thank you for using PyWGCNA.
Would you mind sending me a snapshot of your pyWGCNA_5xFAD.datExpr.var? I wanted to make sure you have a correct gene name column in your dataset.
But overall if you have the correct info in your PyWGCNA object that means there are no GO terms (the cutoff is p-value). you can also do GO analysis directly using functional_enrichment_analysis().
More information: https://github.com/mortazavilab/PyWGCNA/blob/main/tutorials/functional_enrichment_analysis.ipynb
Firstly, thank the author very much. Here is the code.
import PyWGCNA
geneExp = "C:\Users\18308\Desktop\WGCNA\data\data.csv"
pyWGCNA_5xFAD = PyWGCNA.WGCNA(name='data', species='mus musculus', geneExpPath=geneExp, outputPath="C:\Users\18308\Desktop\WGCNA\data\1", save=True, TPMcutoff=0.9) pyWGCNA_5xFAD.geneExpr.to_df().head(5) pyWGCNA_5xFAD.preprocess() pyWGCNA_5xFAD.findModules() pyWGCNA_5xFAD.updateSampleInfo(path="C:\Users\18308\Desktop\WGCNA\data\label1.csv")
add color for metadata
pyWGCNA_5xFAD.setMetadataColor('label', {'0': 'green', '1': 'yellow'})
geneList = PyWGCNA.getGeneList(dataset='mmusculus_gene_ensembl', attributes=['ensembl_gene_id', 'external_gene_name', 'gene_biotype'], maps=['gene_id', 'gene_name', 'gene_biotype'])
pyWGCNA_5xFAD.updateGeneInfo(geneList) pyWGCNA_5xFAD.analyseWGCNA() pyWGCNA_5xFAD.saveWGCNA()
When running the above code, the following prompt appears: No enrich terms when cutoff = 1 in module black No enrich terms when cutoff = 1 in module darkgrey No enrich terms when cutoff = 1 in module darkred No enrich terms when cutoff = 1 in module darksalmon No enrich terms when cutoff = 1 in module firebrick No enrich terms when cutoff = 1 in module indianred No enrich terms when cutoff = 1 in module lightgrey No enrich terms when cutoff = 1 in module mistyrose No enrich terms when cutoff = 1 in module red No enrich terms when cutoff = 1 in module rosybrown No enrich terms when cutoff = 1 in module salmon No enrich terms when cutoff = 1 in module silver No enrich terms when cutoff = 1 in module whitesmoke
Why is this? How can I change cutoff?