Fixes need for Matrix objects as output of assay

[nhejazi]

This PR fixes the issue reported in #42, which caught an out-of-date use of t() on the object produced by SummarizedExperiment::assay(), which (at least as of Bioconductor 3.7) returns an object of class DataFrame. In biomarkertmle(), t() and other downstream functions (e.g., limma::normalizeBetweenArrays()) require a Matrix-like object, a status for which DataFrame apparently does not qualify. This has been fixed by adding an explicit call to as.matrix. The opportunity is also taken to amend documentation and make other less-intrusive packaging changes.

Changes

• explicitly coerce object returned by assay() to class Matrix
• documentation updates + updates to pkgdown site
• names of .R files have been amended for the sake of clarity
• explicitly require all of S4Vectors via @import to satisfy pkgdown

[nhejazi]

Merging despite failure on Bioc-devel.

[nhejazi]

Closes #42