Description Usage Arguments Value References See Also Examples
checknet
takes the inferred mutual information matrix and the true network for validation. - see details.
1 | checknet( finalrelationmatrix, realrelationmatrix)
|
finalrelationmatrix |
The inferred symmetric mutual information matrix, where i,j th element is the mutual information I(i,j) or I(j,i) between two variables i and j. The diagonal is set to zero. |
realrelationmatrix |
A symmetric reference connection matrix, where a 1 at i,j th element defines the connection between variables i and j and non-connection is represented by 0. The diagonal is all zero. |
checknet
returns a vector with 6 elements, that contains the parameters as output <- c(precision, Fscore, recall, TP, FP, FN).
G. Altay, F. Emmert-Streib, "Inferring the conservative causal core of gene regulatory networks", BMC Systems Biology, (2010) 4:132.
makemim
, copula
, c3
, c3net
, c3
, makemim
, copula
, sigtestp
, sigtestMTC
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | data(expdata)
data(truenet)
expdata <- copula(expdata)
mim <- makemim(expdata)
Ic <- 2 #Example cut-off value for mutual information for the first step of C3NET
mim[mim < Ic] <-0 #nonsignificant values eliminated wrt C3NET step 1.
net <- c3(mim) # regulatory network inferred (non zero elements stand for links of
# the predicted network)
scores <- checknet(net,truenet)
|
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