plotAMR: Plot aberrantly methylated regions

In BBCG/ramr: Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

Plot aberrantly methylated regions

Description

'plotAMR' uses 'ggplot2' to visualize aberrantly methylated regions (AMRs) at particular genomic locations.

Usage

plotAMR(
  data.ranges,
  data.samples = NULL,
  amr.ranges,
  highlight = NULL,
  title = NULL,
  window = 300
)

Arguments

data.ranges	A 'GRanges' object with genomic locations and corresponding beta values included as metadata.
data.samples	A character vector with sample names (a subset of metadata column names) to be included in the plot. If 'NULL' (the default), then all samples (metadata columns) are included.
amr.ranges	An output of 'getAMR' - a 'GRanges' object that contain aberrantly methylated regions (AMRs).
highlight	An optional list of samples to highlight. If NULL (the default), will contain sample IDs from the 'sample' metadata column of 'amr.ranges' object.
title	An optional title for the plot. If NULL (the default), plot title is set to a genomic location of particular AMR.
window	An optional integer constant to expand genomic ranges of the 'amr.ranges' object (the default: 300).

Details

For every non-overlapping genomic location from 'amr.ranges' object, 'plotAMR' plots and outputs a line graph of methylation beta values taken from 'data.ranges' for all samples from 'data.samples'. Samples bearing significantly different methylation profiles ('sample' column of 'amr.ranges' object) are highlighted.

Value

The output is a list of 'ggplot' objects.

See Also

getAMR for identification of AMRs, getUniverse for info on enrichment analysis, simulateAMR and simulateData for the generation of simulated test data sets, and 'ramr' vignettes for the description of usage and sample data.

Examples

  data(ramr)
  plotAMR(ramr.data, ramr.samples, ramr.tp.unique[1])
  library(gridExtra)
  do.call("grid.arrange",
          c(plotAMR(ramr.data, ramr.samples, ramr.tp.nonunique), ncol=2))

BBCG/ramr documentation built on June 19, 2022, 11 p.m.