rnb.plot.region.profiles {RnBeads} | R Documentation |
Creates a composite plot showing the sample and groupwise smoothed estimates of methylation values accross all regions of the specified type
rnb.plot.region.profiles( rnb.set, group.index.list, region.type = "", region.profile = NULL, extend.by = 0.33, cvalues = rnb.getOption("colors.category") )
rnb.set |
RnBSet object |
group.index.list |
a list (preferably named) containing sample indices for each group
a list of such lists is for instance generated by the |
region.type |
Region type for which the plot should be generated |
region.profile |
Alternative to specifying |
extend.by |
A number between 0 and 1 specifying the percentage by which a region is extended in order to capture methylation information before region start and after region end |
cvalues |
Color values that will be assigned to sample groups |
a ggplot2 object for plotting the plot shows the smoothed methylation levels of sites accross the specified region type for all regions of that type from 0 (region start) to 1 (region end). Sites in the flanking areas are also shown (coordinates <0 and >1). Smoothing is stratified by sample (dashed lines) and sample group (thick solid lines). Cubic splines are used for smoothing
Fabian Mueller
#Careful: this might take a while library(RnBeads.hg19) data(small.example.object) logger.start(fname=NA) rnb.plot.region.profiles(rnb.set.example,rnb.sample.groups(rnb.set.example)[[1]],"genes")