grin.stats.lsn.plot: GRIN Statistics Lesions Plot

In GRIN2: Genomic Random Interval (GRIN)

GRIN Statistics Lesions Plot

Description

Function return a plot with all types of lesions that spans either a gene or regulatory feature of interest with GRIN statistics added.

Usage

grin.stats.lsn.plot(grin.res, feature = NULL, lsn.clrs = NULL, expand = 5e-04)

Arguments

grin.res	GRIN results for genes or regulatory features (output of the grin.stats function)
feature	Feature ensembl ID from Ensembl regulatory build or FANTOM5 project. An ensembl ID of a gene can be provided as well.
lsn.clrs	Assigned colors per lesion types. If not specified, colors will be automatically assigned using default.grin.colors function.
expand	Controls ratio of the feature locus (start and end position) to the whole plot with default value = 0.0005 (setting expand=0 will only plot the locus from the start to the end position without any of the upstream or downstream regions of the feature).

Details

Function return a plot with all lesions that affect either a gene regulatory feature of interest. Top panel of the plot will has all different types of lesions affecting the loci color coded according to the figure legend. Lower panel of the plot has all the GRIN statistics of the feature that include number of subjects affected by each type of lesions, -log10 p, and –log10q values showing if the feature is significantly affected by the corresponding lesion category. This plot has no panel for transcripts table as regulatory features typically do not have this kind of information.

Value

Function return a plot with all types of lesions that spans either a gene or regulatory feature of interest in addition to the locus GRIN statistics without adding the transcripts panel.

Author(s)

Abdelrahman Elsayed [e-mail] and Stanley Pounds [e-mail]

References

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)

# run GRIN analysis
grin.results=grin.stats(lesion.data,
                        hg19.gene.annotation,
                        hg19.chrom.size)

# Plots showing different types of lesions and GRIN stats for a gene of interest (WT1):
grin.stats.lsn.plot(grin.results,
                     feature="ENSG00000184937")

# same function can be used to plot lesion data and GRIN statistics of regulatory features
# that typically do not have transcripts track to add to the plot.

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