rnb.plot.locus.profile {RnBeads} | R Documentation |
Computes methylation distributions for various region types and sample groups
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" )
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 |
plot.m.heatmap |
flag indicating whether sites methylation values should be displayed in a heatmap. If |
plot.m.smooth |
flag indicating whether a scatterplot with smoothing curves should be displayed. If |
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
|
a ggplot2
plot object containing the plot
Fabian Mueller
#see RnBeads vignette (section: 'Generating Locus Profile Plots') for examples