Reduced imports to 20 and moved the remainder of packages into suggests. Fixed whole genome map. *Optimized load time to plot a whole genome map (should be roughly a 50% reduction, according to profvis).
*Removed Biostrings dependency to clear NOTE (although packages that CNVScope depends on require it). The prior Biostrings issue has been fixed.
Added an explicit dependency, Biostrings to keep CRAN check errors on debian from occurring. Made a small fix to rebinGenomicInteractions, fixing a check at the end to handle a vector input **This will make the package compatible with R 4.0.
*Removed all blockseg references in code. It was a nice feature to have a third algorithm, but blockseg will not be on CRAN shortly.
*Removed blockseg as a strong dependency, per CRAN.
Updated documentation (some new images have been added to show the effect of bin sizes and resolution). Fixed a broken URL that was causing a CRAN note.
Updated documentation for finely binned matrices (see the input matrix vignette). Several sizes of NBL whole genome matrices are available within the package (1e5,2.5e5,1e6,1e7,1e8). These are for package use only. The HD matrices are not speed-optimal for app use. Functionality of basic package functions remains the same as 2.7.2.5. *passes CRAN checks again with flying colors (no notes, warnings, or errors).
Added P-value filter Added correlatoin options Added additional app visualization options. Added material on how to make higher resolution maps.
*Minor changes to package dependency CNVScopePublicData.
*Another minor cran fix to CNVScopeserver.
*Small changes to CNVScopeserver to fix a CRAN check.
Small changes in 2.4.9 to the README, for publicity. Major changes to many functions to pass CRAN checks (global variable issues). CNVScope v2.4.8 (Release date: 2019-07-17) ============== *Small changes to dependencies (including pwr package) and vignettes.
*Minor fix to freadGDCfile documentation
More information about BLCA, SKCM, and AML in additional examples vignette Their processed files have been placed within the package These are available only on the github site as the CRAN size limitations forbid it. Added the ability to specify chrM and chrY in formSampleMatrixFromRawGDCData function.
Changes: * Fixed vignettes not properly linking to the package. CNVScope v2.4.4 (Release date: 2019-07-09) ==============
Changes: