The function maPerm() with save=TRUE will save permutations into RData files. Move all these RData files into the same directory, and indicate this directory using "dir". The output from maPermMerge() will be a list of DMRs detected in all permutations, and can be given to maPermFdr() to compute false discovery rates (FDRs).
Directory containing RData files saved by maPerm() where save was equal to TRUE
A list of DMRs arising from each permutation or bootstrap, merged across all the detected RData files.
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