View source: R/genomewide.log10q.plot.R
genomewide.log10q.plot | R Documentation |
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).
genomewide.log10q.plot(
grin.res,
lsn.grps,
lsn.colors = NULL,
max.log10q = NULL
)
grin.res |
GRIN results object (output from |
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 |
max.log10q |
Numeric; maximum value for -log10(q-value) displayed on the plot. Any value above this threshold will be capped at |
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).
A genome-wide plot showing -log10(q-values) for genes or lesion boundaries associated with specific lesion types.
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org
grin.lsn.boundaries
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).
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