A quick scan of the code tells me it is generally clean and well organized. I read the vignettes and spot-checked a few files in more detail. Below I've listed a few minor issues with file names and line numbers relative to commit 7d0f6da.
spelling and grammar
[x] length.R:82 "... to simplify tha process for large objects .."
[x] union.R:8; AllGenerics.R:303,325,348,368,388 TidySets", should be TidySet
[ ] basic.Rmd:56 "... for each element or set it can be used added:"
[x] vignettes/basic.Rmd:220 "to where it is" should be "of where it is"
[x] vignettes/fuzzy.Rmd:38 Missing period at end of sentence.
[x] vignettes/fuzzy.Rmd:169/175 "type do we have" should be "type we have"
miscellaneous
[x] length.R:199 remove # browser() line
[x] subtract.R:15 remove # browser() line
[x] GMT.R:4 Define the term GMT.
I'm a bioinformatician and I am not familiar with the format, so I think adding a little detail would help. At minimum, you can expand the short description from "Import GMT files" to "Import GMT (Gene Matrix Transposed) files", this at least gives users something to google.
[x] GMT.R:7 "Separation of the file" should be "GMT file field separator"
[x] GMT.R:8,20 The documentation says "..." is passed to strsplit, but in the
code "..." is passed to readLines
[x] naming.R:57,74 & should be &&, since these is a scalar comparison
Line-by-line comments
A quick scan of the code tells me it is generally clean and well organized. I read the vignettes and spot-checked a few files in more detail. Below I've listed a few minor issues with file names and line numbers relative to commit 7d0f6da.
spelling and grammar
miscellaneous