wj2.permuted: The null distribution and p-value

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

The number of permutations

contrast

A two- or three- dimensional vector the contrast(s) for the class differences

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

Value

An n by nB matrix with its columns as the statistic Wj 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).

Examples

Run this code


## 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)
# 
## ---------------------------------------------