grin.oncoprint.mtx: GRIN OncoPrint-Compatible Lesion Matrix

In GRIN2: Genomic Random Interval (GRIN)

GRIN OncoPrint-Compatible Lesion Matrix

Description

Prepares a binary lesion matrix based on GRIN analysis results that can be directly used as input for the oncoPrint function from the ComplexHeatmap package. This matrix summarizes the presence or absence of lesion types across patients for a user-defined list of genes.

Usage

grin.oncoprint.mtx(grin.res, oncoprint.genes)

Arguments

grin.res	A data frame of GRIN results, typically generated by the grin.stats function.
oncoprint.genes	A character vector of Ensembl gene IDs specifying the genes to include in the OncoPrint.

Details

This function filters the GRIN results for a specified set of genes (using their Ensembl IDs), and constructs a gene-by-patient binary matrix indicating the presence of one or more lesion types per gene. Each row represents a gene, each column a patient, and the matrix values reflect whether that gene is affected by any lesion in the given patient.

The output matrix is fully compatible with the oncoPrint() function from the ComplexHeatmap package and allows visualization of lesion patterns across a defined gene set.

This is particularly useful for visualizing mutation, copy number alterations and other structural rearrangements in driver genes or genes selected by statistical criteria (e.g., significance threshold from GRIN results).

Value

A binary data frame (matrix) of dimensions length(oncoprint.genes) and number of patients, suitable for use with the oncoPrint() function.

Author(s)

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

References

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

See Also

grin.stats, oncoPrint

Examples

data(lesion_data)
data(hg38_gene_annotation)
data(hg38_chrom_size)

# Run GRIN analysis
grin.results <- grin.stats(lesion_data,
                           hg38_gene_annotation,
                           hg38_chrom_size)

# Define a list of genes (using Ensembl IDs) to include in the OncoPrint
oncoprint.genes <- c("ENSG00000148400", "ENSG00000171862", "ENSG00000171843",
                     "ENSG00000156531", "ENSG00000162367", "ENSG00000096968",
                     "ENSG00000105639", "ENSG00000118513", "ENSG00000102974",
                     "ENSG00000133703")

# Alternatively, select genes with multiple lesion types and significant q-values
genes.const <- grin.results$gene.hits[grin.results$gene.hits$q2.nsubj < 0.01, ]
selected.genes <- as.vector(genes.const$gene)

# Generate OncoPrint-compatible lesion matrix
oncoprint.mtx <- grin.oncoprint.mtx(grin.results, oncoprint.genes)

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