How do I extract the p-value from runTest() in the TopGO package?
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2.3 years ago
ktm • 0

I am testing a series of gene sets for GO-over-representation using the TopGO package. As algorithm I am using "weight01", statistic: fisher Once I have called runTest I generate the resultstable using the "GenTable()" function. The resulting table contains Go-terms, Term discription, number of anotations per tem, number of significant matches, expected and weightFisher. I would how ever like to be able to filter my data on the p-value per GO term. Do you know how to generate this from the test function?

R TopGo Statistics • 1.2k views
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I think, the column weightFisher contains the p-value.

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2.3 years ago

Please read the manual, before using the package. Copy/pasted the manual ( https://bioconductor.org/packages/release/bioc/vignettes/topGO/inst/doc/topGO.pdf ):

For accessing the GO term’s p-values from a topGO result object the user should use the score functions

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