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#This file belongs to
#netmes: NETMES, <http://www.bioconductor.org/packages/release/Software.html>
#This R package allows local network based assesments for
##inferring regulatory networks from expression data.
## Copyright (C) August 2009 Frank Emmert-Streib and Gokmen Altay
##<v@bio-complexity.com>
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU LESSER GENERAL PUBLIC LICENSE
## as published by the Free Software Foundation; either version 3
## of the License, or any later version.
##
## This program is distributed WITHOUT ANY WARRANTY;
## You can get a copy of the GNU LESSER GENERAL PUBLIC LICENSE
## from
## http://www.r-project.org/Licenses/LGPL-3
evalnetworksNames <- function(E, net, infilepath, namesSif){
file.adr <- paste(infilepath, "1/mim.exp", sep = "");
cc <-read.table(file.adr)
G <- dim(cc)[1] # number of genes is assigned inside the local function
tnet <- abs(net) + abs(t(net)) # true network (make symmetric)
tnet <- 1*(tnet > 0) # in case there were bi-directional connections
cc <- 0
Fscores <- c()
Ithreshold <- c()
mat <- matrix(0, ncol = G, nrow = G)
matgALL <- matrix(0, ncol = G, nrow = G)
for(i in 1:E){
print(i)
infile <- paste(infilepath, as.character(i), "/mim.exp", sep = "")
matf <- readNamesMI(infile, infilepath, namesSif)
m <- max(matf)
if(m == Inf){ # filter problem values
print("problem")
#break
}
else{
cc <- cc + 1
mat <- mat + matf
res <- validate(inet = matf, tnet = tnet)
#options(warn = 1)
fs <- fscores(res, beta = 1)
ind <- which( fs == max(fs))[1] # use the first
Ithr <- res[ind,1]
matg <- (matf >= Ithr)*1
matgALL <- matgALL + matg
Fscores <- append(Fscores, fs[ind], after = length(Fscores))
Ithreshold <- append(Ithreshold, Ithr, after = length(Ithreshold))
}
#if(i == 11)break
}
mat <- mat/cc # averaged mutual information matrix
ratematgALL <- matgALL/cc # rate matrix
indedges <- which(abs(net) > 0, arr.ind = TRUE)
TPReALL <- ratematgALL[indedges]
indedges <- which(abs(net) == 0, arr.ind = TRUE)
FNReALL <- ratematgALL[indedges]
evalnetres <- new.env() # prepare output
assign("aveMImat", mat, envir=evalnetres)
assign("rmat", ratematgALL, envir=evalnetres)
assign("tpre", TPReALL, envir=evalnetres)
assign("fnre", FNReALL, envir=evalnetres)
assign("Fscores", Fscores, envir=evalnetres)
assign("Ithr", Ithreshold, envir=evalnetres)
assign("net", net, envir=evalnetres)
evalnetres
}
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