Question: How do I extract the p-value from runTest() in the TopGO package?
0
gravatar for ktm
3 months ago by
ktm0
ktm0 wrote:

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?

statistics topgo R • 137 views
ADD COMMENTlink written 3 months ago by ktm0

I think, the column weightFisher contains the p-value.

ADD REPLYlink written 3 months ago by e.rempel890
1
gravatar for cpad0112
3 months ago by
cpad011214k
India
cpad011214k wrote:

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

ADD COMMENTlink modified 3 months ago by Kevin Blighe65k • written 3 months ago by cpad011214k
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