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

In EBcoexpress: EBcoexpress for Differential Co-Expression Analysis

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

Returns invisble(NULL)

Author(s)

John A. Dawson <[e-mail]>

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))

EBcoexpress documentation built on Nov. 8, 2020, 7:47 p.m.