al2na
Reduce number of dependencies
Based on the new badge showing all package deps https://bioconductor.org/packages/release/bioc/html/methylKit.html#since introduced on Bioc we are having 87 deps in total.
I was dazzled to see that we have ggplot2 (plus bunch of its deps) in this list, as we are not using it, but this is required by qvalue package as it seems.
That means we can probably reduce our deps by half if we put the qvalue package into the suggests namespace and explicitly check for it on function calls. Anyways, people with the package already installed won't check the difference, it will be just for us to have less deps that can break our releases.
Dependencies can be easily tracked with https://cran.r-project.org/web/packages/miniCRAN/vignettes/miniCRAN-dependency-graph.html .