scores.wire: The weighted contrast

In EMMIXcontrasts2: Contrasts in Mixed Effects for EMMIX Model with Random Effects 2

Description

This function caculates the weighted contrast W_j in order to find out the most significant dfferentially expressed genes.

Usage

scores.wire(obj,contrast=NULL)

Arguments

obj	The return list of function emmixwire
contrast	The vector of the specified contrast

Details

The number of classes of samples is either two or three.

Value

The vector of the statistic Wj

See Also

wire.init.fit,scores.wire.

Examples

## Not run: 

dat <- read.table("GSE36703_37628_col.txt",header=FALSE,sep='\t')

rownames(dat) <- 1:nrow(dat)

###normalize the rows
x <- DoRows(dat)

set.seed(12345)

ret <-emmixwire(x,g=3,ncov=3,nvcov=1,n1=5,n2=6,n3=3,
		debug=1,itmax=1000,epsilon=1e-5)

###calculate the W_j
wj <- scores.wire(ret,contrast=c(0.5,0.5,-1))


## End(Not run)

EMMIXcontrasts2 documentation built on May 30, 2017, 3 a.m.