order.index.gene.data: Order and Index Gene Annotation Data

In GRIN2: Genomic Random Interval (GRIN)

Order and Index Gene Annotation Data

Description

This function orders and indexes gene annotation data by chromosome, gene start, and gene end positions. It is typically used to prepare gene data for overlap analyses with lesion data.

Usage

order.index.gene.data(gene.data)

Arguments

gene.data

A data.frame containing gene annotation information, either provided by the user or retrieved using the get.ensembl.annotation function from the GRIN2.0 package. The data.frame must contain four columns: "gene" Ensembl gene ID. "chrom" Chromosome on which the gene is located. "loc.start" Start position of the gene. "loc.end" End position of the gene.

Value

A list with two components:

gene.data	The input gene annotation data, ordered by chromosome and genomic coordinates.
gene.index	A data.frame with two columns (row.start and row.end) indicating the row indices for genes on each chromosome.

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.

Examples

data(hg38_gene_annotation)

ordered.genes <- order.index.gene.data(hg38_gene_annotation)

GRIN2 documentation built on June 17, 2025, 9:11 a.m.