write.grin.xlsx: Write GRIN Results

In GRIN2: Genomic Random Interval (GRIN)

Write GRIN Results

Description

The function Write GRIN results to an excel file with multiple sheets that include GRIN results, lesion data, gene annotation data, chromosome size, gene-lesion overlap and methods paragraph.

Usage

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

Arguments

grin.result	output results of the grin.stats function.
output.file	output file name ".xlsx".

Value

This function return an excel file with seven sheets that include:

gene.hits	data table of GRIN results that include gene annotation, number of subjects affected by each lesion type for example gain, loss, mutation, etc.., and number of hits affecting each locus. The GRIN results table will also include P and FDR adjusted q-values showing the probability of each locus of being affected by one or a constellation of multiple types of lesions.
gene.lsn.data	each row represent a gene overlapped by a certain lesion. Column "gene" shows the overlapped gene ensembl ID and "ID"" column has the patient ID.
lsn.data	input lesion data
gene.data	input gene annotation data
chr.size	data table showing the size of the 22 autosomes, in addition to X and Y chromosomes in base pairs.
interpretation	provides some details about the content of each sheet in the output excel file and interpretation of each column in the "gene.hits" GRIN results table.
method.paragraph	include a paragraph that explains the GRIN model and cite some references.

Author(s)

Stanley Pounds [e-mail]

References

Pounds, Stan, 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(hg19.gene.annotation)
data(hg19.chrom.size)

# to directly retreive gene annotation and chromosome size files from Ensembl BioMart database,
# UCSC genome browsers and run the GRIN analysis:
grin.results=grin.stats(lesion.data,
                         hg19.gene.annotation,
                         hg19.chrom.size)

# Write GRIN results in to an excel sheet ".xlsx" using write.grin.xlsx function.

GRIN2 documentation built on April 4, 2025, 1:41 a.m.