wj2.permuted: The null distribution and p-value

In EMMIXcontrasts: Contrasts in mixed effects for EMMIX model with random effects.

Description

This function caculates the null distribution and p-values of the weighted contrast W_j.

Usage

wj2.permuted(data,ret,nB=99,contrast=NULL) 
pvalue.wire(wj,wj0)	

Arguments

data	The dataset, an n by m numeric matrix, where n is number of observations and m the dimension of data
ret	The return list of function emmixwire
nB	The number of permutations
contrast	A two- or three- dimensional vector the contrast(s) for the class differences
wj	An n-dimensional vector containing the value of the statistic W_j for each gene
wj0	An n by nB matrix with its columns as the statistic W_j for each permutation

Details

The number of classes of samples is either two or three, and the default contrast for two classes is c(1,-1), and three classes c(1,0,-1).

Value

An n by nB matrix with its columns as the statistic Wj for each permutation.

See Also

emmixwire,scores.wire.

Examples

## Not run: 

dat <- read.table("GSE36703_37628_col.txt",header=FALSE,sep='\t')
rownames(dat) <- 1:nrow(dat)
set.seed(12345)
ret <-emmixwire(dat,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))

### the null distribution of W_j
wj0 <- wj2.permuted(dat,ret,nB=19)
### the p-values of W_j
pv  <- pvalue.wire(wj,wj0)


## End(Not run)

EMMIXcontrasts documentation built on April 14, 2017, 3:25 p.m.