geneRegulationPlot: Gene Regulation Plot

In ZarnackGroup/BindingSiteFinder: Binding site defintion based on iCLIP data

Gene Regulation Plot

Description

Display the fold-change of all binding sites from a given gene on a relative per-nucleotide scale. Binding sites are displayed as dots and with increasing log2 fold-change, they deviate stronger from the center line.

Usage

geneRegulationPlot(
  object,
  plot.geneID = NULL,
  anno.annoDB = NULL,
  anno.genes = NULL,
  match.geneID = "gene_id",
  match.geneName = "gene_name",
  plot.gene.n.tiles = 100,
  alpha = 0.05,
  lfc.cutoff = 2,
  transcript.regions.outlier.handle = c("first", "second", "both", "remove"),
  quiet = FALSE
)

Arguments

object	object; a BSFDataSet object
plot.geneID	character; the gene id of the gene to display. The id must match with the gene ids given in the annotation object.
anno.annoDB	object; an object of class OrganismDbi that contains the gene annotation (!!! Experimental !!!).
anno.genes	object; an object of class GenomicRanges that represents the gene ranges directly.
match.geneID	character; meta column name of the gene ID
match.geneName	character; meta column name of the gene name
plot.gene.n.tiles	numeric; number of tiles the gene should be split in
alpha	numeric; the alpha value to show significantly regulated binding sites. This should match the alpha value used in calculateBsFoldChange.
lfc.cutoff	numeric; log2 fold-change cutoff to show significantly regulated binding sites. This should match the lfc.cutoff value used in calculateBsFoldChange.
transcript.regions.outlier.handle	character; the option how to handle multiple transcript region annotations being present for the same binding site.
quiet	logical; whether to print messages

Details

For this function to work, binding sites must be assigned to hosting genes using assignToGenes. It is also recommended to assing binding sites to transcript regions with assignToTranscriptRegions.

It is also necessary to calculate the log2 fold-change of binding sites between two conditions using the differential binding workflow calculateBsFoldChange.

If in addition the transcript regions of the binding sites are given, then shapes are changed accordingly. An edge case can arise from the merging of two BSFDataSet objects. If binding sites are overlapping and slightly offset close to the end of a particular transcript region annotation, they might be assigned to different regions in both objects. This results in some ambiguity after the merge, where for instance a binding site can be assigned to CDS and 3'UTR. To handle how such edge cases are displayed, the transcript.regions.outlier.handle exists. As default, simply the region of the object that was merged first is shown. If one is interested in showing all regions, then the options both displays both annotations at the same time and labels them accordingly.

Value

an object of class ggplot2

See Also

BSFind, calculateBsFoldChange assignToGenes assignToTranscriptRegions

Examples

# load clip data
files <- system.file("extdata", package="BindingSiteFinder")
load(list.files(files, pattern = ".rda$", full.names = TRUE))
load(list.files(files, pattern = ".rds$", full.names = TRUE)[1])
load(list.files(files, pattern = ".rds$", full.names = TRUE)[2])

# make testset
bds = makeBindingSites(bds, bsSize = 7)
bds = assignToGenes(bds, anno.genes = gns)
bds = assignToTranscriptRegions(object = bds, anno.transcriptRegionList = regions)
bds = imputeBsDifferencesForTestdata(bds)
bds = calculateBsBackground(bds, anno.genes = gns, use.offset = FALSE)

# use all filters and remove binding sites that fail (default settings)
bds = filterBsBackground(bds)

# calculate fold-changes
bds = calculateBsFoldChange(bds)

# make example plot
exampleGeneId = "ENSG00000253352.10"
geneRegulationPlot(bds, plot.geneID = exampleGeneId, anno.genes = gns)

ZarnackGroup/BindingSiteFinder documentation built on April 14, 2025, 1:56 p.m.