GRIN2 (version 2.0.0)

write.grin.xlsx: Write GRIN Results to Excel File

Description

Writes GRIN results to an Excel file containing multiple sheets. The output includes the GRIN summary statistics, input data (lesion and gene annotation), chromosome sizes, gene-lesion overlaps, and explanatory metadata to help with the results interpretation.

Usage

write.grin.xlsx(grin.result, output.file)

Value

The function creates a multi-sheet Excel file at the specified location. The file contains the following sheets:

• gene.hits: The GRIN results table. Includes gene annotation, number of subjects affected by each lesion type (e.g., gain, loss, mutation), total lesion hits per gene, and associated p-values and FDR-adjusted q-values for the probability of lesion enrichment.

• gene.lsn.data: A table where each row corresponds to a lesion overlapping a specific gene. Columns include "gene" (Ensembl gene ID) and "ID" (patient identifier).

• lsn.data: The input lesion dataset used in the GRIN analysis.

• gene.data: The input gene annotation dataset, typically retrieved from Ensembl.

• chr.size: A table listing the size (in base pairs) of chromosomes 1:22, X, and Y.

• interpretation: A guide to understanding the structure and content of each sheet, with detailed descriptions of columns in the gene.hits results table.

• method.paragraph: A summary of the GRIN methodology, including relevant references for citation.

Arguments

grin.result

A list returned by the grin.stats function, containing GRIN analysis output.

output.file

A character string specifying the name of the output Excel file. Must end with ".xlsx".

Author

Abdelrahman Elsayed and Stanley Pounds

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

grin.stats

Examples

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

# Run GRIN analysis using lesion, gene, and chromosome size data:
grin.results <- grin.stats(lesion_data,
                           hg38_gene_annotation,
                           hg38_chrom_size)

# Write results to an Excel file:
tmp_file <- file.path(tempdir(), "GRIN_Results.xlsx")
write.grin.xlsx(grin.results, output.file = tmp_file)
if (file.exists(tmp_file)) file.remove(tmp_file)