RnBeads (version 1.4.0)

rnb.plot.locus.profile: rnb.plot.locus.profile

Description

Computes methylation distributions for various region types and sample groups

Usage

rnb.plot.locus.profile(rnbSet, chrom, start, end, grps = NULL, plot.m.regions = NULL, plot.m.heatmap = TRUE, plot.m.smooth = TRUE, cvals.grps = rnb.getOption("colors.category"), cvals.meth = rnb.getOption("colors.meth"), smooth.profile = "wide")

Arguments

rnbSet

RnBSet object

chrom

chromosome of window to plot

start

start coordinate of window to plot

end

end coordinate of window to plot

grps

a list of indices for each group to be compared or NULL if no sample grouping information should be displayed

plot.m.regions

character vector of region types whose methylation values should be displayed If grps is not NULL the methylation values will be separated by sample groups.

plot.m.heatmap

flag indicating whether sites methylation values should be displayed in a heatmap. If grps is not NULL the heatmaps will be separated by sample groups.

plot.m.smooth

flag indicating whether a scatterplot with smoothing curves should be displayed. If grps is not NULL the colors will be used to separate sample groups.

cvals.grps

colors to be used for the different groups

cvals.meth

colors to be used for methylation values and heatmaps

smooth.profile

profile to be used for the smoothing curves. Allowed values include wide (default) which yields smoother curvers and narrow which yields more "wiggly" curves

Value

a ggplot2 plot object containing the plot

Examples

#see RnBeads vignette (section: 'Generating Locus Profile Plots') for examples