1.2.0

Please also update reference data-packages to their latest version to work with this version of RAPToR

• Introduced a reference (ref) object and corresponding make_ref() and print functions. ref objects to
  • make reference-building more direct, from a geim object,
  • simplify the age estimation call (now simply ae(samp, ref)),
  • store reference metadata (such as the reference time unit) for use in subsequent plotting/printing.
• Updated ae object printing to include reference metadata when available.
• Optimized ae bootstrap correlation (>2x faster)
• Rewrote ae plotting function to
  • display bootstrap estimates by default.
  • include reference time units when available.
  • fix ae plotting graphics bug (larger first plot with overlayed and missing elements) when displaying multiple plots side by side.
  • add sample label control (truncate, adjust margin space)
  • cover more parameter edge cases
• Updated geim printing to include reference metadata when available.
• Added functions to compare log-fold-changes between sample groups to a reference and quantify the impact of development on differential expression analysis.
  • ref_compare() gets matching reference time points to the samples and compares logFCs between given sample groups, and between matching reference time points (giving an estimate of development logFCs between groups).
  • get_logFC() extracts sample and reference logFCs between specified groups from the output of ref_compare().
• Renamed plot_cor.ae() to plot_cor().
• Removed deprecated plotting function for df_CV
• Updated vignette documentation:
  • Added a vignette on correcting DE analysis for development vignette("RAPToR-DEcorrection")
  • Updated vignette sections related to reference-building with the new objects.
  • Added a reference-building section and example for aging references
  • Re-formatted vignettes with Bioconductor style
  • Added PDF versions of all vignettes (index entries with -pdf, e.g. vignette("RAPToR-pdf"))