NEWS

SGSeq 1.10.0

New vignette
Changes in the SGVariants and SGVariantCounts class. Instances created with previous versions of SGSeq have to be updated.
Replaced functions for accessing assay data with two generic functions counts() and FPKM()
Support BamFileLists in sample info
Changed behavior of the annotate() function when assigning gene names
Changed behavior of the min_denominator argument in analyzeVariants() and getSGVariantCounts(). The specfied minimum count now has to be achieved at either the start or end of the event.
Adjacent exons no longer cause a warning in convertToTxFeatures()
Deprecated legacy classes TxVariants, TxVariantCounts
Bug fixes and other improvements

Added importTranscripts() for importing annotation from GFF format
Added plotCoverage() for visualization of per-base read coverage and junction read counts
Added predictVariantEffects() for predicting the effect of splice variants on annotated protein-coding transcripts
findSGVariants() is now able to deal with more complex gene models
SGVariants columns closed5p and closed3p now refer to individual splice variants rather than the splice event they belong to
Bug fixes and other improvements

Renamed class TxVariants to SGVariants
Renamed class TxVariantCounts to SGVariantCounts
Renamed findTxVariants() to findSGVariants()
Renamed getTxVariantCounts() to getSGVariantCounts()
Parallelization is now controlled with a single cores argument
Argument max_complexity for predictTxFeatures() controls skipping of problematic regions
getBamInfo() is no longer run as part of analyzeFeatures()
getSGVariantCounts() now supports obtaining counts from BAM files
Bug fixes and other improvements