GRIN2

New features

• Added exon-level target-size modeling to grin.stats() for user-selected lesion types through the new exons.annotation, exon.chrom.size, and exon_level arguments. Lesion types not selected for exon-level modeling continue to use conventional gene- and chromosome-level target sizes, allowing both approaches to be used in the same analysis.
• Added grin.logRank() for gene-level association analyses between genomic lesion groups and time-to-event outcomes using gene-by-subject lesion-group matrices, such as those generated by prep.lsn.type.matrix(). This function complements the existing grin.assoc.lsn.outcome() workflow for binary gene-lesion matrices generated by prep.binary.lsn.mtx() to evaluate associations with binary and time-to-event outcomes through logistic regression and Cox proportional hazards models, respectively.
• Added grin.assoc.expr.outcome() for gene-level association analyses between gene expression and clinical outcomes. The function fits Cox proportional hazards models for time-to-event outcomes and logistic regression models for binary outcomes, with optional covariate adjustment.

Improvements

• Updated the grin.stats() pipeline so that selected lesion types can be modeled using the annotated exon target size of each gene together with the total annotated exonic target size of the corresponding chromosome. This approach is especially useful when analyses are restricted to protein-altering exonic variants, such as missense, nonsense, and coding frameshift variants, and for studies based on whole-exome sequencing. Other lesion types can continue to use conventional gene- and chromosome-level target sizes within the same analysis.
• Updated get.ensembl.annotation() to retrieve versioned, pre-generated GRCh38 Ensembl annotation bundles containing gene, exon, and regulatory-element annotations. Downloaded resources can be cached locally, are verified using MD5 checksums, and are reused when valid, reducing dependence on live Ensembl BioMart availability and improving reproducibility.
• Updated lsn.transcripts.plot() to support flexible gene-centered and user-defined regional plots, transcript selection and labeling, improved rendering of point-like and interval-like lesions, refined track layout and alignment, customizable lesion colors, and expanded plotting controls.
• Updated onco.print.props() to preserve user-specified color palettes.
• Updated grin.oncoprint.mtx() to use Ensembl gene IDs when gene symbols are unavailable, preserve user-specified gene order, and ensure unique gene labels in OncoPrint matrices.
• Updated write.grin.xlsx() to exclude the gene.lsn.data worksheet, reducing workbook size and improving export performance.
• Standardized and clarified the expr.mtx documentation across expression-analysis functions, including the expected gene-by-subject orientation, identifier requirements, and numeric expression-value requirements.