GRIN2 2.0.0

Major updates

• Significant improvements to the prob.hits() function, greatly enhancing the performance and speed of probability convolution calculations for measuring statistical significance of lesion frequencies.
• Removed the row.bern.conv() function and introduced pbc() and rpbc(), which compute the probability that a series of independent Bernoulli trials yields x or more successes.
• Improved compatibility with the Human GRCh38 (hg38) genome assembly.
• Some packages that handle Human GRCh37 (hg19) assembly annotations are either outdated or have platform compatibility issues. Therefore, the support for hg19 has been discontinued in get.ensembl.annotation() and lsn.transcripts.plot(). These functions now exclusively support hg38, and users are encouraged to convert their lesion data coordinates to hg38 before running GRIN2 analyses.

New features

• Enhanced error handling with informative messages for missing annotations or data inputs.
• Added a new vignette, GRIN2, which demonstrates the package’s preprocessing, analysis, and plotting capabilities.

Data and Annotation

• Included bundled datasets for GRCh38: lesion_data, expr_data, hg38_gene_annotation, hg38_chrom_size, and hg38_cytoband.
• Ensembl and regulatory annotations are retrieved directly from Ensembl BioMart v110 with graceful fallback mechanisms.

Bug fixes and improvements

• Improved Roxygen documentation for better CRAN compliance.
• get.ensembl.annotation() and get.chrom.length() now handle database connection issues with informative error messages.
• Fixed minor bugs in genomewide.lsn.plot(), specifically regarding color assignment for lesion groups when not automatically specified by default.grin.colors().