mle.getEncodingLength {CTD}R Documentation

Minimum encoding length

Description

This function calculates the mininmum encoding length associated with a subset of variables given a background knowledge graph.

Usage

mle.getEncodingLength(bs, pvals, ptID, G)

Arguments

bs

- A list of bitstrings associated with a given patient's perturbed variables.

pvals

- The matrix that gives the perturbation strength significance for all variables (columns) for each patient (rows)

ptID

- The row name in data.pvals corresponding to the patient you specifically want encoding information for.

G

- A list of probabilities with list names being the node names of the background graph.

Value

df - a data.frame object, for every bitstring provided in bs input parameter, a row is returned with the following data: the patientID; the bitstring evaluated where T denotes a hit and 0 denotes a miss; the subsetSize, or the number of hits in the bitstring; the individual p-values associated with the variable's perturbations, delimited by '/'; the combined p-value of all variables in the set using Fisher's method; Shannon's entropy, IS.null; the minimum encoding length IS.alt; and IS.null-IS.alt, the d.score.

Examples

# Identify the most significantly connected subset for a given patients'
# perturbations, given the network G
data("Miller2015")
data_mx = Miller2015[-c(1,grep("x - ",rownames(Miller2015))),
                        grep("IEM", colnames(Miller2015))]
data_mx = apply(data_mx, c(1,2), as.numeric)
data_pval=t(apply(data_mx,c(1,2),
                    function(i)2*pnorm(abs(i),lower.tail=FALSE)))
# Choose patient #1's (i.e., IEM_1000's) top 5 perturbed metabolites
ptID = colnames(data_mx)[1]
S=rownames(data_mx)[order(abs(data_mx[,which(colnames(data_mx)==ptID)]),
                            decreasing=TRUE)[seq_len(5)]]
# Build a dummy metabolite network for all metabolites in data_mx
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)
ranks = list()
for (n in seq_len(length(S))) { 
    print(sprintf("%d / %d", n, length(S)))
    ind = which(names(G)==S[n])
    ranks[[n]]=singleNode.getNodeRanksN(ind,G,p1=0.9,thresholdDiff=0.01,
                                        adj_mat,S,log2(length(G)),FALSE) 
}
names(ranks) = S
ptBSbyK = mle.getPtBSbyK(S, ranks)
res = mle.getEncodingLength(ptBSbyK, data_pval, ptID, G)
# Rows with d.scores > 4.32 are of interest. Anything less indicates
# no to weak signal.
res = res[order(res[,"d.score"], decreasing=TRUE),]
print(res)

[Package CTD version 1.0.0 Index]