grin.results: Example GRIN2 Analysis Results

In GRIN2: Genomic Random Interval (GRIN)

Example GRIN2 Analysis Results

Description

A precomputed GRIN2 results object generated from the example genomic lesion dataset included with the package. The object represents a standard gene-level GRIN2 analysis and is provided for use in examples of downstream analysis, visualization, and export functions without repeatedly running grin.stats().

Format

A named list containing the following 10 components:

gene.hits

A data frame containing the primary GRIN2 analysis results for each gene, including lesion counts, affected-subject counts, lesion-specific probabilities, p-values, q-values, and constellation test statistics.

lsn.data

The genomic lesion dataset used as input to grin.stats. Each row corresponds to a genomic lesion together with its genomic coordinates, lesion type, and subject identifier.

gene.data

The gene annotation data used during the analysis, including genomic coordinates and gene identifiers.

gene.lsn.data

A data frame describing overlaps between genomic lesions and genes.

chr.size

Chromosome target sizes used for probability calculations.

gene.index

Internal index used to efficiently identify chromosome-specific groups of genes during the analysis.

lsn.index

Internal index used to efficiently identify chromosome-specific groups of genomic lesions during the analysis.

gene.exon.size

Gene-specific exon target sizes used for exon-level analyses. This component is NULL for the standard gene-level example.

exon.chrom.size

Chromosome exon target sizes used for exon-level analyses. This component is NULL for the standard gene-level example.

exon_level

Indicates which lesion types were modeled using exon-level target sizes. This component is NULL for the standard gene-level example.

Details

The object was generated using:

grin.results <- grin.stats(
  lsn.data = lesion_data,
  gene.data = hg38_gene_annotation,
  chr.size = hg38_chrom_size
)

This dataset is intended primarily for package examples and demonstrations. It allows downstream GRIN2 functions to be illustrated without repeatedly running grin.stats. The object contains the complete output returned by grin.stats and can therefore be supplied directly to functions that require a GRIN2 results object.

Source

Generated from the example datasets lesion_data, hg38_gene_annotation, and hg38_chrom_size included with the GRIN2 package.

See Also

grin.stats, lsn.transcripts.plot, grin.oncoprint.mtx, write.grin.xlsx

Examples

data("grin.results")

# Display the available components.
names(grin.results)

# View the first few rows of the primary results table.
head(grin.results$gene.hits)

GRIN2 documentation built on Aug. 22, 2026, 5:09 p.m.