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@@ -40,12 +40,14 @@ for fedup pathway enrichment analysis. Current file formats supported are
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40
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40
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gmt, txt, and xlsx.
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}
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\examples{
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+# Generate pathway list from GMT annotation file
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pathways <- readPathways(
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system.file("extdata", "Human_Reactome_November_17_2020_symbol.gmt",
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package = "fedup"
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),
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minGene = 10, maxGene = 500
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)
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+# Generate pathway list from XLSX annotation file
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pathways <- readPathways(
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system.file("extdata", "SAFE_terms.xlsx", package = "fedup"),
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header = TRUE, pathCol = "Enriched.GO.names", geneCol = "Gene.ID"
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