Nothing
## Analyse mcmc output
read.chain <- function(output.folder, chainNumber)
{
runinfo <- read.table(paste(output.folder, "/runInfo.txt", sep=""), as.is=T)[,1]
geneNames <- read.table(paste(output.folder, "/geneNames.txt", sep=""), as.is=T)[,1]
if (runinfo[1] == "LinearNet")
{
chainOut <- .read.linear.chain(output.folder, chainNumber, geneNames)
}
if (runinfo[1] == "NonLinearNet")
{
chainOut <- .read.splines.chain(output.folder, chainNumber, geneNames)
}
if (runinfo[1] == "ReplicatesNet_student")
{
chainOut <- .read.reps_student.chain(output.folder, chainNumber, geneNames)
}
if (runinfo[1] == "ReplicatesNet_gauss")
{
chainOut <- .read.reps_gauss.chain(output.folder, chainNumber, geneNames)
}
chainOut
}
## Function to build vector of all-interactions lables
.lablesGammaChain <- function(geneNames)
{
fullLabels <- NULL
for (i in geneNames)
{
fullLabels_i <- paste(i, "regs", geneNames, sep ="-")
fullLabels <- c(fullLabels, fullLabels_i)
}
fullLabels
}
.read.linear.chain <- function(output.folder, chainNumber, geneNames)
{
all.interactions.Labels <- .lablesGammaChain(geneNames)
chain.name <- paste("chain", chainNumber, sep="")
file.name.1 <- paste(output.folder, "/", chain.name, sep="")
## Check if chain exists, if not exit
chainExists <- .checkChainExists(output.folder, chain.name)
if(!chainExists){stop("Chain does not exist")}
## Read data
fixedGammaMat <- as.matrix(read.table(paste(file.name.1, "/FixedGammaFile", sep="")))
lambda.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_mcmc", sep=""))
colnames(lambda.mcmc.1) <- geneNames
mu.1 <- .readFast(paste(file.name.1, "/Mu_mcmc", sep=""))
colnames(mu.1) <- geneNames
ro.1 <- .readFast(paste(file.name.1, "/Rho_mcmc", sep=""))
gamma.1 <- .readFast(paste(file.name.1, "/Gamma_mcmc", sep=""))
notfixed.indx <- !is.finite(fixedGammaMat)
colnames(gamma.1) <- all.interactions.Labels[notfixed.indx]
coeff.1 <- .readFast(paste(file.name.1, "/B_mcmc", sep=""))
reg.indx <- which(notfixed.indx | fixedGammaMat == 1)
colnames(coeff.1) <- all.interactions.Labels[reg.indx]
list(lambda = lambda.mcmc.1, mu = mu.1, rho = ro.1,
gamma = gamma.1, coeff = coeff.1)
}
.read.splines.chain <- function(output.folder, chainNumber, geneNames)
{
all.interactions.Labels <- .lablesGammaChain(geneNames)
chain.name <- paste("chain", chainNumber, sep="")
file.name.1 <- paste(output.folder, "/", chain.name, sep="")
## Check if chain exists, if not exit
chainExists <- .checkChainExists(output.folder, chain.name)
if(!chainExists){stop("Chain does not exist")}
## Read data
fixedGammaMat <- as.matrix(read.table(paste(file.name.1, "/FixedGammaFile", sep="")))
lambda.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_mcmc", sep=""))
colnames(lambda.mcmc.1) <- geneNames
mu.1 <- .readFast(paste(file.name.1, "/Mu_mcmc", sep=""))
colnames(mu.1) <- geneNames
ro.1 <- .readFast(paste(file.name.1, "/Rho_mcmc", sep=""))
gamma.1 <- .readFast(paste(file.name.1, "/Gamma_mcmc", sep=""))
notfixed.indx <- !is.finite(fixedGammaMat)
colnames(gamma.1) <- all.interactions.Labels[notfixed.indx]
tau.1 <- .readFast(paste(file.name.1, "/Tau_mcmc", sep=""))
reg.indx <- which(notfixed.indx | fixedGammaMat == 1)
colnames(tau.1) <- all.interactions.Labels[reg.indx]
all.f.1 <- read.table(paste(file.name.1, "/all_f", sep=""))
all.interactions.Labels.trans <- as.vector(t(matrix(all.interactions.Labels,length(geneNames),length(geneNames))))
colnames(all.f.1) <- all.interactions.Labels.trans
all.fsqr.1 <- read.table(paste(file.name.1, "/all_f_sqr", sep=""))
colnames(all.fsqr.1) <- all.interactions.Labels.trans
list(lambda = lambda.mcmc.1, mu = mu.1, rho = ro.1,
gamma = gamma.1, tau = tau.1, all.f = all.f.1,
all.fsqr = all.fsqr.1)
}
.read.reps_gauss.chain <- function(output.folder, chainNumber, geneNames)
{
all.interactions.Labels <- .lablesGammaChain(geneNames)
chain.name <- paste("chain", chainNumber, sep="")
file.name.1 <- paste(output.folder, "/", chain.name, sep="")
## Check if chain exists, if not exit
chainExists <- .checkChainExists(output.folder, chain.name)
if(!chainExists){stop("Chain does not exist")}
## Read data
fixedGammaMat <- as.matrix(read.table(paste(file.name.1, "/FixedGammaFile", sep="")))
lambda.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_mcmc", sep=""))
colnames(lambda.mcmc.1) <- geneNames
mu.1 <- .readFast(paste(file.name.1, "/Mu_mcmc", sep=""))
colnames(mu.1) <- geneNames
ro.1 <- .readFast(paste(file.name.1, "/Rho_mcmc", sep=""))
gamma.1 <- .readFast(paste(file.name.1, "/Gamma_mcmc", sep=""))
notfixed.indx <- !is.finite(fixedGammaMat)
colnames(gamma.1) <- all.interactions.Labels[notfixed.indx]
coeff.1 <- .readFast(paste(file.name.1, "/B_mcmc", sep=""))
reg.indx <- which(notfixed.indx | fixedGammaMat == 1)
colnames(coeff.1) <- all.interactions.Labels[reg.indx]
Y.1 <- read.table(paste(file.name.1, "/Y_mean", sep=""))
rownames(Y.1) <- geneNames
lambda.exp.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_exp_mcmc", sep=""))
colnames(lambda.exp.mcmc.1) <- geneNames
# X.1 <- as.vector(as.matrix(read.table(paste(file.name.1, "/DataMean_standarised", sep=""))))
X.1 <- as.matrix(read.table(paste(file.name.1, "/DataMean_standarised", sep="")))
rownames(X.1) <- geneNames
list( lambda = lambda.mcmc.1, mu = mu.1, rho = ro.1,
gamma = gamma.1, coeff = coeff.1, Y = Y.1,
lambda.exp = lambda.exp.mcmc.1, X_mean = X.1)
}
.read.reps_student.chain <- function(output.folder, chainNumber, geneNames)
{
all.interactions.Labels <- .lablesGammaChain(geneNames)
chain.name <- paste("chain", chainNumber, sep="")
file.name.1 <- paste(output.folder, "/", chain.name, sep="")
## Check if chain exists, if not exit
chainExists <- .checkChainExists(output.folder, chain.name)
if(!chainExists){stop("Chain does not exist")}
## Read data
fixedGammaMat <- as.matrix(read.table(paste(file.name.1, "/FixedGammaFile", sep="")))
lambda.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_mcmc", sep=""))
colnames(lambda.mcmc.1) <- geneNames
mu.1 <- .readFast(paste(file.name.1, "/Mu_mcmc", sep=""))
colnames(mu.1) <- geneNames
ro.1 <- .readFast(paste(file.name.1, "/Rho_mcmc", sep=""))
gamma.1 <- .readFast(paste(file.name.1, "/Gamma_mcmc", sep=""))
notfixed.indx <- !is.finite(fixedGammaMat)
colnames(gamma.1) <- all.interactions.Labels[notfixed.indx]
coeff.1 <- .readFast(paste(file.name.1, "/B_mcmc", sep=""))
reg.indx <- which(notfixed.indx | fixedGammaMat == 1)
colnames(coeff.1) <- all.interactions.Labels[reg.indx]
Y.1 <- read.table(paste(file.name.1, "/Y_mean", sep=""))
rownames(Y.1) <- geneNames
lambda.exp.mcmc.1 <- .readFast(paste(file.name.1, "/Lambda_exp_mcmc", sep=""))
colnames(lambda.exp.mcmc.1) <- geneNames
X.1 <- as.vector(as.matrix(read.table(paste(file.name.1, "/DataMean_standarised", sep=""))))
rownames(X.1) <- geneNames
deg.1 <- .readFast(paste(file.name.1, "/DegFreedom_mcmc", sep=""))
colnames(deg.1) <- geneNames
acceptanceRatio.1 <- read.table(paste(file.name.1, "/acceptanceRatio", sep=""))[,1]
list( lambda = lambda.mcmc.1, mu = mu.1, rho = ro.1,
gamma = gamma.1, coeff = coeff.1, Y = Y.1,
lambda.exp = lambda.exp.mcmc.1, X_mean = X.1, degFreedom = deg.1,
acceptanceRatio = acceptanceRatio.1)
}
.checkChainExists <- function(output.folder, chain.name)
{
dir.out <- dir(output.folder)
indx.chain <- grep(chain.name, dir.out)
return(length(indx.chain) > 0)
}
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.