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YuanTian1991 / ChAMP

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champ.EpiMod function not found #28

Open drhmoosavi opened 2 years ago

drhmoosavi commented 2 years ago

Hi, I am running the champ.process function as below: champ.process(directory = getwd(), arraytype="EPIC", runimpute=T, runDMP=FALSE, runRefBase=FALSE, runGSEA=FALSE, Rplot = FALSE, PDFplot=T, runQC= T)

I get the following error message Error in champ.EpiMod(beta = myNorm, pheno = tmppd$Sample_Group, nseeds = 100, : could not find function "champ.EpiMod". I can't find the function in help either. Any thoughts ?

drhmoosavi commented 2 years ago

Running the same code above, I also encounter this error (when runEpiMod= FALSE )

`Running champ.CNA()... [===========================] [<<<<< ChAMP.CNA START >>>>>] champ.CNA Results will be saved in ./CHAMP_CNA .

ChaMP.CNA does not provide batch Correct on intensity data now, but you can use champ.runCombat to correct slides batch yourself. << Create Control Data >> << Combining champ bloodCtl dataset into your intensity dataset as control >> Error in ctlIntensity[rownames(intensity), ] : subscript out of bounds`

drhmoosavi commented 2 years ago

when saving the result of champ.process function in "champres" I get the following errors when: try to run champ.ebGSEA gseares <- champ.ebGSEA(beta=champres$champ.impute$beta, pheno=champres$champ.load$pd$Sample_Group, minN=10, adjPval=0.05, arraytype="EPIC", cores=4)

ebGSEA function require no NA in beta and pheno parameter. [ Section 1: Generate Annotation Start ] Extracting annotation from IlluminaHumanMethylationEPICilm10b4.hg19. Removing Non-CG probes out of annotation. Flat all genes on each CpG. Removing all duplicated CpG-genes. Annotation Prepared. [ Section 1: Generate Annotation Done ] [ Section 2: Running Global Test Start ] Applying Binary Model on Global Test. It could be very slow... Error in eval(family$initialize) : y values must be 0 <= y <= 1 In addition: Warning message: In alias2SymbolTable(flat$symbol) : Multiple symbols ignored for one or more aliases

442330994 commented 1 year ago

Yes i have encountered with the same problem.

Error in champ.EpiMod(beta = myNorm, pheno = group_list) : could not find function "champ.EpiMod"