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I greatly appreciate the funciton, just quickly pointing an minor issue - a confusing warning message.
Gene list with n < 25 may have insufficent power for enrichment analysis followed by gene lists with more than 25 genes.
These genes lists are more than 25.
There is due to an inconsistency between the min_gene at 25, and the actually checking of the gene sets which is 200. see the following code section
spatialLIBD/R/gene_set_enrichment.R
Lines 86 to 94 in 8c0fcd8
| min_genes <- 25 | |
| if (any(geneList_length < min_genes)) { | |
| warning( | |
| "Gene list with n < ", | |
| min_genes, | |
| " may have insufficent power for enrichment analysis: ", | |
| paste(names(geneList_length)[geneList_length < 200], collapse = " ,") | |
| ) | |
| } |
I appreciate your listening, and hard work on the package!
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