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are either outdated or have platform compatibility issues.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().