order.index.lsn.data: Order and Index Lesion Data

In GRIN2: Genomic Random Interval (GRIN)

Order and Index Lesion Data

Description

This function orders and indexes lesion data by lesion type, chromosome, and subject ID. It prepares lesion data for downstream GRIN analysis by structuring it in a way that facilitates efficient access and overlap computations.

Usage

order.index.lsn.data(lsn.data)

Arguments

lsn.data

A data.frame containing lesion data formatted for GRIN. It must include the following five columns: "ID" Patient identifier. "chrom" Chromosome on which the lesion is located. "loc.start" Start position of the lesion. "loc.end" End position of the lesion. "lsn.type" Lesion type (e.g., gain, loss, mutation, fusion, etc...).

Value

A list with two elements:

lsn.data	The input lesion data, ordered by lesion type, chromosome, and subject.
lsn.index	A data.frame with two columns, row.start and row.end, indicating the index range of lesions for each subject-lesion type-chromosome combination. For example, if a patient has a single deletion on chromosome 5, row.start will equal row.end. If there are four deletions, the range will span four rows.

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(lesion_data)

ordered.lsn <- order.index.lsn.data(lesion_data)

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