- Small edit to configuration files that address compilation issues that can arise on some systems. Deals with “file too big” errors” during package installation from source.
- Implemented long read sequencing data analysis strategy. Run bakRFit() with Long = TRUE to use k-means clustering (k = 2) for mutation rate and fraction new estimation. Need to have Ckmeans.1d.dp package installed to do this (not installed during bakR installation).
- Fixed bug in reliableFeatures. high_p was supposed to be the maximum allowable mutation rate (# of mutations/# of Ts) in reads from -s4U controls, but was instead the maximum allowable average number of T-to-C mutations in reads from these controls.
- Fixed bug in cBprocess that didn’t properly check that features of interest provided by the FOI argument were valid.
CRAN release: 2023-03-14
- Added QC_check(), a function to perform quality control analysis with bakRFit objects. Looks for any problems in your data that will impair bakR’s performance, generates a number of diagnostic visualizations, and makes suggestions about what to do next.
- Fixed plot coloring bug in plotMA() and plotVolcano().
- Fixed bug that led to problems when the number of -s4U replicates > +s4U replicates in one or more Exp_IDs
- Implemented improved U-content adjustment for MCMC implementation. Also impacts accuracy of StanRateEst = TRUE mutation rate estimation strategy.
- Increased default number of features to use for StanRateEst mutation rate estimation strategy.
- Improved scaling of NSSHeat() output matrix columns.
- Created a new function NSSHeat2() that implements a different mechanism scoring function than NSSHeat().
- Optimized data preprocessing with data.table
- Increased simulation flexibility
- Added edge case error catching
- Added checks to bakRData validator
- Fixed bug in NSSHeatmap that prevented adjusting padj cutoff
CRAN release: 2022-10-10
- Addressed NOTEs to prepare for CRAN submission
- Removed previously deprecated function sim_bakRData()
- Fixed non-steady-state (NSS) uncertainty quantification
- Fixed uncertainty quantification for pulse-chase analysis
- Fixed fraction new estimation for pulse-chase analysis
- Improved default mutation rate estimation strategy
- Updated vignettes and added back non-steady state analysis strategy discussion
- Better commenting of fast_analysis (instead of opting for refactorization)
- Changed ordering of vignettes on website
- Got rid of unnecessary stan models and functions
- Fixed TL_stan output documentation
- Corrected missing namespace issues