plotMostDiscordant: Plot a heatmap showing a selection of loci

Description Usage Arguments Value Author(s) Examples

View source: R/plotMostDiscordant.R

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

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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 <t.peters@garvan.org.au>

Examples

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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)

timpeters82/consensus documentation built on May 23, 2020, 12:45 a.m.