The function reconstructs a new methylBase object from an input methylBase object and percent methylation matrix. Basically, it uses the read coverages in the input methylBase object and deduces new number of methylated Cs and unmethylated Cs based on the input percent methylation matrix. It is ideally to be used to reconstruct methylBase objects after batch correction on percent methylation values. The percent methylation matrix rows must match methylBase object rows in order ,and in addition column order (the order of samples) in input methylBase must match the order in percent methylation matrix.
percent methylation matrix, row order and order of the samples same as the methylBase object
methylBase object where methylation
percentage matches input
methMat and coverages
Batch effect correction (if any batch effect exists) is a
tricky issue. We provide some simple ways to deal with it
), But if you can find other ways to correct for batch
effects and want to create a methylBase object with the
corrected percent methylation values, you can use this
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data(methylKit) # get percent methylation mat=percMethylation(methylBase.obj) # do some changes in the matrix # this is just a toy example # ideally you want to correct the matrix # for batch effects mat[mat==100]=80 # reconstruct the methylBase from the corrected matrix newobj=reconstruct(mat,methylBase.obj)
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