Improvements for version 1.2

[llrs]

List of improvements for the release 1.2

Vignettes

1. • Remove wall of text when loading Org.Hs.eg.db via suppressPackageStartupMessages
2. • Remove merging similarities explanation in the vignette
3. • Call GOSemSim in the vignette instead of comparing with static/hard coded values
4. • Make a note to section 9.8 about clashing namespace
5. • Remove cluster description in the GOSemSim comparison
6. • Section 9.3 move last sentence as a note
7. • Correct title of section 9.8 / Check grammar
8. • [] Add advanced vignette (currently hosted in here)
     8.1. - [x] Add the packages needed as suggested
     8.2. - [x] Remove section 1.2 but keep the subset of genes
     8.3. - [x] Explain better the implication of the tests.
     8.4. - [x] Compare the similarity within the DE genes and between DE subset and the others
     8.5. - [x] Maybe a plot of one similarity and the other

Package

1. • Reduce memory foot print
2. • Reduce time for building in Windows

[llrs]

Memory footprint hasn't be reduced (in parallel it stills eats all the memory) This will require use of RCpp or a change in how combineScoresPar works.

[llrs]

I thought that introducing parallel calculus would reduce memory foot print. Obviously (now) I know it doesn't. I tried addressing some speed and inefficiencies in the code but it wasn't enough to compute the gene similarities for all genes in reactome.db ~ 1041.

Possible steps would be to improve internal memory usage and using Rcpp package and similar packages (and finally learning c++).