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Error while calculating differentially methylated regions(dmrs) after SWAN normalization in minfi for methylation array data

Hi,

I am unable to extract differentially methylated regions(dmrs) after SWAN normalization in minfi for methylation array data.

Below is the code used:

MSet.swan <- preprocessSWAN(RGset)
beta_N <- getBeta(MSet.swan)

Sample_Group <- pData(MSet.swan)$Sample_Group 

dmp <- dmpFinder(beta_N, pheno = Sample_Group , type = "categorical") 
write.csv(dmp, file="C:/Users/sinha.puja/Desktop/baseDir2/Exporteddmp-SWAN.csv", row.names=T)
pheno <- pData(MSet.swan)$Sample_Group
pheno
designMatrix <- model.matrix(~ pheno)
designMatrix
*dmrs <- bumphunter(MSet.swan, design = designMatrix, cutoff = 0.2, B=0, type="Beta")*

I got the following error at the dmrs step:

Error in (function (classes, fdef, mtable)  : 
 unable to find an inherited method for function ‘bumphunter’ for signature ‘"MethylSet"’.

If anyone is familiar with this type of error and knows how to solve this then please please help..!!!!

Thanks.

r
• 1,557 views • link
written by sinha.puja • sinha.puja

There are so many subject matter keywords and specific technologies in the question, yet the only tag used is R. Why is that, OP? Please edit your question and add relevant tags.

• 0 views • link
written by Ram Ram

I do not know that tool but these kinds of error indicate that the MSet.swan is not the input format that bumphunter() is expectig. Check ?bumphunter towards the correct input for the function.

• 0 views • link
written by ATpoint ATpoint

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