panelPlots {skewr} | R Documentation |
Creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes(Pidsley,2013) as a series of 'tick' marks located above the x-axis.
panelPlots(MethyLumiSet, typeIRedModels, typeIGreenModels, typeIIModels, plot = c("panel", "frames"), samp.num = NULL, frame.nums = 1:9, norm = "", idmr = TRUE, snps = TRUE)
MethyLumiSet |
The |
typeIRedModels |
A |
typeIGreenModels |
A |
typeIIModels |
A |
plot |
Should the output consist of panel plots–one panel per sample or a single panel if |
samp.num |
If plotting for a single sample is desired, for which sample. The number given simply refers to the |
frame.nums |
if |
norm |
A character string which will be displayed as part of the main title for each plot. Useful in indicated which normalization method was used for the modeled and plotted data |
idmr |
logical; should the intensities of the idmr probes be plotted as a series of tick-marks above the x-axis. The default is |
snps |
logical; should the intensities of the rs probes be plotted as a series of tick-marks above the x-axis. The default is |
No return value. Only plots are generated.
Please refer to the vignette for an example workflow.
Ryan Putney ryanputney@gmail.com
Prates MO, Cabral CRB, Lachos VH (2013).mixsmsn: Fitting Finite Mixture of Scale Mixture of Skew-Normal Distributions. Journal of Statistical Software, 54(12), 1-20. http://www.jstatsoft.org/v54/i12/
if(require('minfiData')) { path <- system.file("extdata/5723646052", package="minfiData") methylumiset.raw <- getMethyLumiSet(path = path) mixes.raw.meth.I.red <- getSNparams(methylumiset.raw, 'M', 'I-red') mixes.raw.meth.I.green <- getSNparams(methylumiset.raw, 'M', 'I-green') mixes.raw.meth.II <- getSNparams(methylumiset.raw, 'M', 'II') mixes.raw.unmeth.I.red <- getSNparams(methylumiset.raw, 'U', 'I-red') mixes.raw.unmeth.I.green <- getSNparams(methylumiset.raw, 'U', 'I-green') mixes.raw.unmeth.II <- getSNparams(methylumiset.raw, 'U', 'II') mixes.I.red <- list(mixes.raw.meth.I.red, mixes.raw.unmeth.I.red) mixes.I.green <- list(mixes.raw.meth.I.green, mixes.raw.unmeth.I.green) mixes.II <- list(mixes.raw.meth.II, mixes.raw.unmeth.II) panelPlots(methylumiset.raw, mixes.I.red, mixes.I.green, mixes.II) }