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markrobinsonuzh / DAMEfinder

Finds DAMEs - Differential Allelicly MEthylated regions
MIT License
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fix MDSplot based on limma commit #39

Closed sorjuela closed 3 years ago

sorjuela commented 3 years ago

Change required based on:

commit 1e27129c2640f8e7112844715037c345c59e1312 Author: Gordon Smyth smyth@wehi.edu.au Date: Sun Mar 28 16:08:37 2021 +1100

 28 Mar 2021: limma 3.47.12

 - Rewrite the MDS calculations performed by plotMDS(). The function no
   longer calls cmdscale() but instead performs the necessary
   eigenvector computations directly. Proportion of variance explained
   by each dimension is now computed. The `ndim` argument is now
   removed. All eigenvectors are now stored so that plotMDS.MDS does
   not need to recompute them if different dimensions are requested.