plotEmpiricalDistribution: Plot the empirical distribution of the methylation beta vals...

In kdkorthauer/dmrseq: Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing

Plot the empirical distribution of the methylation beta vals or coverage

Description

Uses ggplot2 to plot smoothed density histograms of methylation proportions (beta values), or coverage. Methylation proportion densities are weighted by coverage. The number of curves plotted will be equal to the number of different values of testCovariate, unless bySample is TRUE. This can take quite some time to execute for a large object, so it is recommended to first take a random sample of loci (say one million) before plotting.

Usage

plotEmpiricalDistribution(
  bs,
  testCovariate = NULL,
  bySample = FALSE,
  type = "M",
  adj = 2.5
)

Arguments

bs	a BSseq object
testCovariate	character specifying the column name of the pData slot of the BSseq object to include in the plot legend.
bySample	logical whether to plot a separate line for each sample, even if the grouping testCovariate is specified. Default value is FALSE (so samples with the same value of testCovariate will be collapsed into the same line). If testCovariate is not specified, this parameter does not have an effect and samples are automatically plotted separately.
type	a character indicating which type of density to plot - the methylation (beta) values ("M") or the coverage ("Cov"). Default is "M".
adj	a numeric value for the adjust parameter to pass to the geom_line function. Specifies how smooth the make the function.

Value

a ggplot object

Examples

data(BS.chr21)

# plot beta values by sample group
plotEmpiricalDistribution(BS.chr21, testCovariate="CellType")

kdkorthauer/dmrseq documentation built on Sept. 26, 2024, 9:32 p.m.