bindingSiteCoveragePlot: Plot signal coverage of selected ranges

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

Plot signal coverage of selected ranges

Description

Function plots the coverage of the CLIP data in the signal slot and plots it as coverage. The plot is centered around a given binding site, which can be selected by an index.

Usage

bindingSiteCoveragePlot(
  object,
  plotIdx,
  flankPos,
  shiftPos = NULL,
  mergeReplicates = FALSE,
  autoscale = FALSE,
  highlight = TRUE,
  showCentralRange = TRUE,
  customRange = NULL,
  customRange.name = "custom",
  customAnnotation = NULL,
  customAnnotation.name = "anno",
  title = NULL,
  colorPalette = NULL
)

Arguments

object	a BSFDataSet object
plotIdx	integer, index of the range to plot
flankPos	numeric, number of nucleotides by which the plotting frame is symmetrically extended
shiftPos	numeric, nucleotide positions by which the current plotting range should be shifted
mergeReplicates	logical, if replicates should be merge per condition (TRUE) or if every replicates should be shown separately (FALSE)
autoscale	logical, if y-axis should be scaled to the maximum for all replicates (TRUE), or not (FALSE)
highlight	logical, if the central range should be highlighted (TRUE), or not (FALSE)
showCentralRange	logical, if the central range should be shown (TRUE), or not (FALSE)
customRange	GenomicRanges, a custom range object to be shown underneath the coverage tracks
customRange.name	character, the name of the customRange track
customAnnotation	GenomicRanges or TxDb, a custom annotation for eg. gene, exons, etc. to be shown underneath the coverage tracks
customAnnotation.name	character, the name of the customAnnotation track
title	character, set plotting title
colorPalette	vector, hex colors used for the conditions

Value

an object of class GVIZ

See Also

BSFDataSet, BSFind

Examples

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

bindingSiteCoveragePlot(bds, plotIdx = 3, flankPos = 10)

ZarnackGroup/BindingSiteFinder documentation built on Nov. 24, 2024, 10:41 a.m.