Nothing
discordance.delta <-
function(x, names = NULL, theta = 0.05, corrected = TRUE,
printToTex = FALSE, directory = NULL, file.name = NULL){
## internal functions ##
delta.prime <-
function(
q,
theta
)
{
sum(q<theta) / length(q)
}
delta <-
function(
rA,
rB,
q,
theta
)
{
sum((rA+rB)*(q<theta)) / (sum(rA) + sum(rB))
}
##############
if(is.null(names)){
samples <- names(x)
}
n.s <- length(x)
out.df <- data.frame(samples = samples,
Delta = 1:n.s,
Delta.prime = 1:n.s)
theta = theta
if (corrected == T){
ind <- 7
}else{
ind <- 3
}
for (i in 1:n.s) {
in.df <- as.data.frame(x[[i]])
out.df$Delta[out.df$samples == samples[i]] <-
delta(
in.df$freqA,
in.df$freqB,
in.df[ind],
theta
)
out.df$Delta.prime[out.df$samples == samples[[i]]] <-
delta.prime(
in.df[[ind]],
theta
)
}
if(printToTex ==T){
if(is.null(file.name)){
file.name = paste("discordanceDelta", ".txt", sep = "" )
}
if(!is.null(directory)){
file.name = paste(directory, "/", file.name, sep = "")
}
table = xtable(out.df, label="tab:Delta", digits = c(3), caption = "$\\Delta$ and $\\Delta'$.")
print(table, file = file.name)
}
return(out.df)
}
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