plotMostDiscordant: Plot a heatmap showing a selection of loci

In consensus: Cross-platform consensus analysis of genomic measurements via interlaboratory testing method

Description

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.

Usage

plotMostDiscordant(consfit, param=c("average", "sensitivity", "precision"), 
                   numloci=20, pal=colorRampPalette(brewer.pal(9, "RdYlGn")))

Arguments

consfit	An object of class ConsensusFit.
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.

Value

A plot to the current device.

Author(s)

Tim Peters <[e-mail]>

Examples

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)

consensus documentation built on Nov. 8, 2020, 8:32 p.m.