Description Usage Arguments Details Value See Also Examples
This function caculates the null distribution and p-values of the weighted contrast W_j.
1 2 | wj2.permuted(data,ret,nB=99,contrast=NULL)
pvalue.wire(wj,wj0)
|
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 |
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).
An n by nB matrix with its columns as the statistic Wj for each permutation.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 | ## 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)
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