LA-methods: Function to calculate LA estimate

Description

'LA' is used to calculate the LA estimate for a gene triplet data.

Arguments

object

An numerical matrix object with three columns or an object of ExpresionSet class with three features.

dim

An index of the column for the gene to be treated as the third controller variable. Default is dim=3

geneMap

A character vector with three elements representing the mapping between gene names and feature names (optional).

Value

'LA' returns a numerical value representing the estimated value. A more detailed explanation of the value is illustrated in the vignette.

Details

The input object can be a numerical matrix with three columns with row representing observations and column representing three variables. It can also be an ExpressionSet object with three features. If input a matrix class data, all three columns of the object representing the variables should have column names. Each variable in the object will be standardized with mean 0 and variance 1 in the function. In addition, the third variable will be quantile normalized within the function. More detail example about the usage of geneMap is demonstrated in the vignette.

References

Ker-Chau Li, Genome-wide coexpression dynamics: theory and application (2002). PNAS 99 (26): 16875-16880.

Yen-Yi Ho, Leslie Cope, Thomas A. Louis, and Giovanni Parmigiani, GENERALIZED LIQUID ASSOCIATION (April 2009). Johns Hopkins University, Dept. of Biostatistics Working Papers. Working Paper 183. http://www.bepress.com/jhubiostat/paper183

Examples

Run this code

data<-matrix(rnorm(300), ncol=3)

colnames(data)<-c("Gene1", "Gene2", "Gene3")

LAest<-LA(data)

LAest