Description Usage Arguments Details Value Note Author(s) References See Also Examples
Determines a statistical p-value that shows the significance of the overlap between two networks.
1 | ganet.FEtest(nOverlap, nPredicted, nFocusedSet, nUniverse)
|
nOverlap |
The number of unique overlap. |
nPredicted |
The number of predcitions. |
nFocusedSet |
The number of elements (interactions) in the database of interest, regarding the genes of raw dataset. |
nUniverse |
The number of biologically possible (expected) interactions regarding the genes of raw dataset . |
This may be used for instance to search for whether the number of predicted gene/protein interactions (nPredicted) are overlapping in a biological interaction database of interest with a significant p-value.
It results an environment 'res' with two output: res$stats and res$precision.
stats |
All the statistical results from Fisher's exact test. |
precision |
The rate of accurate predictions over all the predicted links. |
This package is intended to be updated with respect to feedbacks and also with updates of the current databases.
Gokmen Altay
1. G. Altay, N. Altay, D.E. Neal, Global assessment of network inference algorithms based on available literature of gene/protein interactions, Turk J Biol, 37:547-555, 2013. 2. G. Altay, J Zapardel, B Peters, "Determining preprocessing combinations and sample size for Gene Network Inference over ...", bioArxiv, 2017.
ganet.ComLinks
, ganet.combine
, ganet.UniqNetSimp
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | #data(ganet.ex.net) # assume this is the predicted protein interactions
#data(hprd) # This is the HPRD database to search for in it.
#Validated <- ganet.ComLinks(netlist=as.matrix(ganet.ex.net), netdata=as.matrix(hprd))
#data(ganet.ex.genes) # load the example unique genes of the example
#row dataset to compute the number of universe
#nUniverse <- length(ganet.ex.genes)*(length(ganet.ex.genes) - 1)/2 #
#all possible interactions with these genes.
##This is the upper-bound and over-optimistic.
#We recommend to take no more than half of it.
#nUniverse <- nUniverse/2
#nFocusedSet <- length( intersect( which(hprd[,1] %in% ganet.ex.genes),
#which(hprd[,2]%in% ganet.ex.genes) ) )
#res <- ganet.FEtest(nOverlap=nrow(Validated), nPredicted=nrow(ganet.ex.net),
#nFocusedSet=nFocusedSet, nUniverse=nUniverse)
#res$stats$p.value
#res$precision
|
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