EBcoexpress (version 1.16.0)

makeMyD: A function to convert the X expression matrix into the D correlation matrix

Description

A function to convert the X expression matrix into the D correlation matrix; uses either Pearson's correlation coefficient or biweight midcorrelation

Usage

makeMyD(X, conditions, useBWMC = FALSE, gpsep = "~")

Arguments

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

useBWMC

Should biweight midcorrelation be used instead of Pearson's correlation coefficient?

gpsep

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

Value

A p-by-K matrix of observed correlations for all p gene-pairs, where p is choose(m,2), m is the 1st dimension of X and K is the number of conditions specified by the conditions array

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))
tinyPat <- ebPatterns(c("1,1","1,2"))
D <- makeMyD(fiftyGenes, tinyCond, useBWMC=TRUE)