plotMostDiscordant {consensus} | R Documentation |
Plots a heatmap of a specified number of loci showing per-platform, values for either (a) average (a_i), (b) sensitivity (b_i) or (c) precision (d_i) for the most discordant for each. Discordance is ranked by V(a_i), V(b_i) or \frac{Σ(d_i)}{p-1} where p= the number of platforms/conditions.
plotMostDiscordant(consfit, param=c("average", "sensitivity", "precision"), numloci=20, pal=colorRampPalette(brewer.pal(9, "RdYlGn")))
consfit |
An object of class |
param |
Whether average (a_i), sensitivity (b_i) or precision (d_i) is plotted. |
numloci |
The number of loci to plot. |
pal |
Colour palette. Length must be at least the number of platforms/conditions. |
A plot to the current device.
Tim Peters <t.peters@garvan.org.au>
data("TCGA") tcga_mm <- MultiMeasure(names=c("U133A", "Huex", "Agilent", "RNASeq"), data=list(U133A, Huex, Agilent, RNASeq)) fit <- fitConsensus(tcga_mm) plotMostDiscordant(fit, "sensitivity", 25)