# Get patient distances for the first 2 patients in the Miller 2015 dataset.
data("Miller2015")
data_mx = Miller2015[-c(1,grep("x - ", rownames(Miller2015))),
grep("IEM",colnames(Miller2015))]
data_mx = apply(data_mx[,c(1,2)], c(1,2), as.numeric)
# Build a network, G
adj_mat = matrix(0, nrow=nrow(data_mx), ncol=nrow(data_mx))
rows = sample(seq_len(ncol(adj_mat)), 0.1*ncol(adj_mat))
cols = sample(seq_len(ncol(adj_mat)), 0.1*ncol(adj_mat))
for (i in rows) {for (j in cols) {adj_mat[i,j]=rnorm(1,mean=0,sd=1)}}
colnames(adj_mat) = rownames(data_mx)
rownames(adj_mat) = rownames(data_mx)
G = vector("numeric", length=ncol(adj_mat))
names(G)=colnames(adj_mat)
# Look at the top 5 metabolites for each patient.
kmx=5
topMets_allpts = c()
for (pt in seq_len(ncol(data_mx))) {
topMets_allpts=c(topMets_allpts,
rownames(data_mx)[order(abs(data_mx[,pt]),
decreasing=TRUE)[seq_len(kmx)]])}
topMets_allpts = unique(topMets_allpts)
# Pre-compute node ranks for all metabolites in topMets_allpts
# for faster distance calculations.
ranks = list()
for (n in seq_len(length(topMets_allpts))) {
ind = which(names(G)==topMets_allpts[n])
ranks[[n]]=singleNode.getNodeRanksN(ind,G,0.9,0.01,adj_mat,
topMets_allpts,log2(length(G)))
}
names(ranks) = topMets_allpts
# Also pre-compute patient bitstrings for faster distance calculations.
ptBSbyK = list()
for (pt in seq_len(ncol(data_mx))) {
S=rownames(data_mx)[order(abs(data_mx[,pt]),
decreasing=TRUE)[seq_len(kmx)]]
ptBSbyK[[pt]] = mle.getPtBSbyK(S, ranks)
}
# Build your results ("res") list object to store patient distances at
# different size k's.
res = list()
t = list(ncd=matrix(NA, nrow=ncol(data_mx), ncol=ncol(data_mx)))
rownames(t$ncd) = colnames(data_mx)
colnames(t$ncd) = colnames(data_mx)
for (i in seq_len(kmx)) { res[[i]] = t }
for (pt in seq_len(ncol(data_mx))) {
print(pt)
ptID = colnames(data_mx)[pt]
for (pt2 in pt:ncol(data_mx)) {
ptID2 = colnames(data_mx)[pt2]
tmp=mle.getPtDist(ptBSbyK[[pt]],ptID,ptBSbyK[[pt2]],ptID2,
data_mx,ranks,p1=0.9,thresholdDiff=0.01,adj_mat)
for (k in seq_len(kmx)) {
res[[k]]$ncd[ptID, ptID2] = tmp$NCD[k]
res[[k]]$ncd[ptID2, ptID] = tmp$NCD[k]
}
}
}
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