View source: R/grin.stats.lsn.plot.R
grin.stats.lsn.plot | R Documentation |
Generates a plot showing all lesion types that span a specified gene or regulatory feature with GRIN stats added.
grin.stats.lsn.plot(grin.res, feature = NULL, lsn.clrs = NULL, expand = 5e-04)
grin.res |
GRIN results for genes or regulatory elements, as returned by the |
feature |
Ensembl ID of a feature of interest. This can be either a gene (e.g., Ensembl gene ID) or a regulatory region from Ensembl Regulatory Build or FANTOM5 project. |
lsn.clrs |
Named vector of colors for each lesion type. If not provided, colors are automatically assigned using |
expand |
Numeric value that controls the proportion of the flanking region (upstream/downstream) around the gene to be included. Default is |
The plot consists of two panels:
Top panel: Displays all lesion types overlapping the selected gene or regulatory feature. Lesions are color-coded by type, as indicated in the legend.
Bottom panel: Summarizes GRIN statistics for the feature, including the number of subjects affected per lesion type, and the corresponding -\log_{10}(p)
and -\log_{10}(q)
values for significance.
This plot is particularly useful for regulatory features, which typically lack transcript structure. Therefore, no transcript or exon structure is shown.
A two-panel plot showing lesion distribution and GRIN statistics for a given gene or regulatory feature, without a transcript annotation panel.
Abdelrahman Elsayed abdelrahman.elsayed@stjude.org and Stanley Pounds stanley.pounds@stjude.org
Cao, X., Elsayed, A. H., & Pounds, S. B. (2023). Statistical Methods Inspired by Challenges in Pediatric Cancer Multi-omics.
grin.stats
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)
# Plot lesion and GRIN stats for a gene of interest (e.g., WT1)
grin.stats.lsn.plot(grin.results, feature = "ENSG00000184937")
# Can also be also used for regulatory features without transcript panels
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