genomewide.log10q.plot: Genome-wide -log10(q-value) Plot
In GRIN2: Genomic Random Interval (GRIN)

genomewide.log10q.plot

R Documentation

Genome-wide -log10(q-value) Plot

Description

Generates a genome-wide plot of -log10(q-values) for each annotated gene or lesion boundary evaluated by GRIN. The plot is lesion-type specific (e.g., gain, loss, mutation).

Usage

genomewide.log10q.plot(
  grin.res,
  lsn.grps,
  lsn.colors = NULL,
  max.log10q = NULL
)

Arguments

`grin.res`	GRIN results object (output from `grin.stats`) using either gene annotation or lesion boundaries as marker input.
`lsn.grps`	A character vector specifying which lesion group(s) to include in the plot.
`lsn.colors`	A named vector of colors corresponding to each lesion group. If `NULL`, default colors will be assigned using the `default.grin.colors()` function.
`max.log10q`	Numeric; maximum value for -log10(q-value) displayed on the plot. Any value above this threshold will be capped at `max.log10q`.

Details

This function visualizes the significance of lesions affecting genomic loci across chromosomes. It plots -log10(q-values) for either gene-based or lesion-boundary markers based on the GRIN analysis. The plot is faceted or colored by lesion group (e.g., gain, loss).

Value

A genome-wide plot showing -log10(q-values) for genes or lesion boundaries associated with specific lesion types.

Author(s)

Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org

Examples

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

# Example 1: Use lesion boundaries for gains
gain <- lesion_data[lesion_data$lsn.type == "gain", ]
lsn.bound.gain <- grin.lsn.boundaries(gain, hg38_chrom_size)
GRIN.results.gain.bound <- grin.stats(gain, lsn.bound.gain, hg38_chrom_size)

genomewide.log10q.plot(GRIN.results.gain.bound,
                       lsn.grps = c("gain"),
                       lsn.colors = c("gain" = "red"),
                       max.log10q = 10)

# hg38_gene_annotation can be used instead of the boundaries as the marker data.

# This function can be used similarly for other lesion types (e.g., loss, mutation).

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