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🍪 SEnsible Step-wise Analysis of DNA MEthylation BeadChips
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testEnrichmentFisher function help #135

Open ardan33 opened 10 months ago

ardan33 commented 10 months ago

Hello- I am trying to look at the difference between the normalized sdf's of three doses (Control, Low, High). I have loaded my covariates into the global environment, but I am at a loss as to how the testEnrichmentFisher function works and what the input should be.

I tried: testEnrichmentFisher(sdf_normalized,covariates,universe,alternative="greater")

and got the error that : Error in testEnrichmentFisher(sdf_normalized, covariates, universe, alternative = "greater") : could not find function "testEnrichmentFisher"

I read the sesame pdf and it mentions this function, so I am not sure what package I need to install for the function to exist, as I already installed sesame?

And once I install it, are my inputs correct (where sdf_normalized is the normalized sdf using openSesame, covariates is a matrix (consisting of 36 rows x 6 columns - sentrix_ID, sentrix_position, sample name, sex, sample group, and sampleID (sentrixID+position)). Or am I reading the documentation wrong?

I am newer to using R for bioinformatics so I apologize for my ignorance in understanding this. Thanks for your help as always!

zwdzwd commented 10 months ago

Please use probe ID vector instead of SigDFs for testEnrichment. The probe ID vector can be from DML analysis. We are working on expanding the KYCG documentation. Please stay tuned.