Jenssen-Shannon Divergence Test
라벨:
Informatics
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# Option I (self-made implement)
###
library(microbiome)
library(flexmix)
jsmat <- matrix(NA, nrow = ncol(dat), ncol = ncol(dat))
rownames(jsmat) <- colnames(jsmat) <- colnames(dat)
rd <- relative.abundance(10^dat[mytax,])
for (i in 1:(ncol(dat)-1)) {
for (j in (i+1):ncol(dat)) {
print(c(i,j))
a <- rd[, i]
b <- rd[, j]
s <- (a + b)/2
kldiv.a <- KLdiv(cbind(a, s), eps=10^-4, overlap=TRUE)
kldiv.b <- KLdiv(cbind(b, s), eps=10^-4, overlap=TRUE)
js.ab <- (kldiv.a[1, 2] + kldiv.b[1, 2])/2
jsmat[i, j] <- js.ab
}
}
###
# Option II
###
source("http://www.bioconductor.org/biocLite.R")
biocLite("cummeRbund")
library(cummeRbund)
jsmat2 <- JSdist(rd)
e.g.
mat<-matrix(sample(1:50,50),10)
probs<-makeprobs(mat)
js.distance<-JSdist(probs)
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라벨:
Informatics
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