EBcoexpress (version 1.16.0)

showPair: A function for looking at a pair's differential co-expression

Description

This function plots the expression data for a given pair, coloring by condition. A regression line may be added; this line may be made robust so that it only uses those data points used by biweight midcorrelation

Usage

showPair(pair, X, conditions, gsep = "~", regLine = TRUE, useBWMC = TRUE, colors = NULL, ...)

Arguments

pair

A pair name, such as ABC~XYZ, where ~ is the separator given by gsep

X

An m-by-n expression matrix, where rows are genes and columns are chips (subjects); include all chips in X, indicate condition in the conditions array

conditions

The conditions array

gsep

A separator that indicates a gene-pair, such as P53~MAPK1. The separator should not appear in any of the gene names

regLine

Should a regression line be drawn for each condition?

useBWMC

Should the regression line be robust, a la biweight midcorrelation?

colors

Colors for the different conditions. Defaults to palette()

...

Other options to be passed to plot(), with three exceptions. The lty= and lwd= options will be passed to abline() and will have an effect on the plot when regLine=TRUE; col= is overwritten by the colors= array and may not be specified. All other ... options will be passed to the main plot.

Value

References

Dawson JA and Kendziorski C. An empirical Bayesian approach for identifying differential co-expression in high-throughput experiments. (2011) Biometrics. E-publication before print: http://onlinelibrary.wiley.com/doi/10.1111/j.1541-0420.2011.01688.x/abstract

Examples

data(fiftyGenes)
tinyCond <- c(rep(1,100),rep(2,25))
showPair("X1~X2",fiftyGenes, conditions=tinyCond, pch=20,
  xlim=c(-4,4), ylim=c(-4,4))
#
showPair("X26~X35",fiftyGenes, conditions=tinyCond, pch=20,
  xlim=c(-4,4), ylim=c(-4,4))
#
showPair("X1~X35",fiftyGenes, conditions=tinyCond, pch=20,
  xlim=c(-4,4), ylim=c(-4,4))