Fixed a test
v0.0.78 -- working on the vignette using ggbio as an example
Fixed vignette stubs. Passes devtools::install('derfinder', build_vignettes = TRUE) using CRAN versions of knitrBootstrap and knitcitations
Note on building vignette
Working on vignettes
update travis and R build ignore
Add advanced args for regionReport
v0.0.79 -- Implemented FWER calculation in mergeResults() when optionsStats is provided.
v0.0.80 -- finished introductory vignette (have to test it... but it seems that knitrBoostrap hangs at the pandoc step)
v0.0.81 -- starting work on the advanced vignette
Updated the NEWS for recent changes
improve wording
v0.99.0 -- getting ready for BioC. Still working on advanced vignette
Required derfinderHelper 0.99.0
Updated README. Removed RefManageR which is used in the real vignette, but not on the fake one, and will prompt a warning in R CMD check (I think). Anyhow, it is installed when installing knitcitations so I don't expect this to be a major problem.
Clean up after creating the vignette
Fixed passing of advanced arguments from analyzeChr()
Had to make lowMemDir a regular argument in order to set a different default in analyzeChr() than what is used later on
Fix call to fstats.apply() in calculatePvalues()
Call should be fixed now