find.gene.lsn.overlaps: Find Gene-Lesion Overlaps

In GRIN2: Genomic Random Interval (GRIN)

Find Gene-Lesion Overlaps

Description

Identifies overlaps between genes and genomic lesions using the output from prep.gene.lsn.data(). The function detects instances in which a genomic lesion spans or intersects the genomic coordinates of a gene.

Usage

find.gene.lsn.overlaps(gl.data)

Arguments

gl.data

A list returned by prep.gene.lsn.data() containing processed and indexed gene and lesion data. When exon-level analysis was requested, the list also contains gene- and chromosome-level exon target sizes and the lesion types designated for exon-level analysis.

Details

The function scans the combined gene and lesion position table generated by prep.gene.lsn.data() and identifies lesions that overlap the genomic coordinates of each gene. Each detected gene-lesion overlap is recorded for subsequent counting and statistical analysis.

Gene-lesion overlap detection is unchanged when exon_level is specified and continues to use the complete genomic coordinates of each gene. Exon-level gene and chromosome target sizes do not alter whether a lesion is considered to overlap a gene. Instead, these objects are carried forward for use in downstream GRIN probability calculations. Lesion types specified in exon_level should therefore contain only exonic lesions, as described in prep.gene.lsn.data().

All genes represented in gene.data are included in overlap detection, regardless of whether they have a matching exon annotation. Genes without a valid exon target size remain available for standard GRIN analyses but will not receive probability estimates for lesion types specified in exon_level.

Value

A list containing the following components:

lsn.data

Processed lesion data.

gene.data

Processed gene annotation data.

gene.lsn.data

A data.frame ordered by chromosome and genomic position that contains both gene and lesion boundaries. The cty column identifies the position type: 1 = gene start, 2 = lesion start, 3 = lesion end, and 4 = gene end.

gene.lsn.hits

A data.frame in which each row represents a gene overlapped by a genomic lesion. It contains the gene and lesion row indices, gene identifier and coordinates, patient or sample identifier, lesion coordinates, and lesion type.

gene.index

A data.frame indexing the rows corresponding to genes on each chromosome.

lsn.index

A data.frame indexing lesion groups defined by lesion type, chromosome, and subject.

gene.exon.size

Numeric vector containing the total annotated exon target size for each gene, aligned by gene.row. Genes without a valid matching exon annotation have a value of NA. These genes remain available for standard GRIN analyses but are excluded from probability calculations for lesion types specified in exon_level. Returns NULL when exon-level analysis was not requested.

exon.chrom.size

A data.frame containing the genome-wide annotated exon target size for each chromosome. This object is carried forward for use in downstream exon-level probability calculations. Returns NULL when exon-level analysis was not requested.

exon_level

Character vector specifying the lesion types designated for exon-level analysis. Returns NULL when exon-level analysis was not requested.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

Pounds, S., et al. (2013). A genomic random interval model for statistical analysis of genomic lesion data.

Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.

See Also

prep.gene.lsn.data, count.hits, prob.hits

Examples

data(lesion_data)
data(hg38_gene_annotation)
data(example_exon_annotation)
data(hg38_exon_chrom_size)

# Prepare gene and lesion data using the optional arguments
# for exon-level analysis
prep.gene.lsn <- prep.gene.lsn.data(
  lsn.data = lesion_data,
  gene.data = hg38_gene_annotation,
  exons.annotation = example_exon_annotation,
  exon.chrom.size = hg38_exon_chrom_size,
  exon_level = "mutation"
)

# Identify genes overlapped by genomic lesions
gene.lsn.overlap <- find.gene.lsn.overlaps(prep.gene.lsn)

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