`plotAMR` uses `ggplot2` to visualize aberrantly methylated regions (AMRs) at particular genomic locations.
plotAMR(
data.ranges,
data.samples = NULL,
amr.ranges,
highlight = NULL,
title = NULL,
window = 300
)
A `GRanges` object with genomic locations and corresponding beta values included as metadata.
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.
An output of `getAMR` - a `GRanges` object that contain aberrantly methylated regions (AMRs).
An optional list of samples to highlight. If NULL (the default), will contain sample IDs from the `sample` metadata column of `amr.ranges` object.
An optional title for the plot. If NULL (the default), plot title is set to a genomic location of particular AMR.
An optional integer constant to expand genomic ranges of the `amr.ranges` object (the default: 300).
The output is a list of `ggplot` objects.
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.
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.