Nothing
#this programming used unequal-variance t-test, if use equal-variance t-test, can get little different genelists.
# i.e. in function entity.build2, method = "t.equalvar" instead of "t")
# ref library(multtest) function: mt.teststat
# If test="t", the tests are based on two-sample Welch t-statistics (unequal variances).
# If test="t.equalvar", the tests are based on two-sample t-statistics with equal variance for the two samples. The square of the t-statistic is equal to an F-statistic for k=2.
entitybuild2 <- function (expr.mat, ALLtype = NULL, type, dataset = NULL, minSampleNum = 3,
method = "t", random = FALSE)
{
n.patient <- length(ALLtype)
#cat("entities building")
if (ncol(expr.mat) != length(ALLtype))
stop("expr.mat and ALLtype not match!")
n.type <- length(type)
entity.labels <- array(0, dim = ncol(expr.mat))
for (i in 1:n.type) entity.labels[which(ALLtype == type[i])] <- i
if (n.type == 2) {
i <- 1
j <- 2
if (length(which(entity.labels == i)) > minSampleNum)
if (length(which(entity.labels == j)) > minSampleNum) {
#cat(".")
entity1 <- paste(dataset, type[i], sep = "")
entity2 <- paste(dataset, type[j], sep = "")
groupA <- which(entity.labels == i)
nA <- length(groupA)
if (random) {
groupA <- sample(n.patient, nA)
}
groupB <- which(entity.labels == j)
nB <- length(groupB)
if (random) {
groupB <- (1:n.patient)[-groupA]
}
twogroup <- c(groupA, groupB)
lab <- c(rep(1, nA), rep(0, nB))
t <- mt.teststat(expr.mat[, twogroup], lab, test = method)
entity <- c(entity1, entity2)
}
}
else {
t <- NULL
entity <- NULL
i <- which(type == "CCR")
for (j in (1:n.type)[-i]) {
if (length(which(entity.labels == i)) > minSampleNum)
if (length(which(entity.labels == j)) > minSampleNum)
if (type[j] != "Censored") {
#cat(".")
thisentity1 <- paste(dataset, type[i], sep = "")
thisentity2 <- paste(dataset, type[j], sep = "")
groupA <- which(entity.labels == i)
groupB <- which(entity.labels == j)
twogroup <- c(groupA, groupB)
nA <- length(groupA)
nB <- length(groupB)
if (random) {
groupA <- sample(twogroup, nA)
groupB <- twogroup[!twogroup %in% groupA]
twogroup <- c(groupA, groupB)
}
lab <- c(rep(1, nA), rep(0, nB))
thist <- mt.teststat(expr.mat[, twogroup],
lab, test = method)
t <- cbind(t, thist)
thisentity <- rbind(thisentity1, thisentity2)
entity <- cbind(entity, thisentity)
}
}
}
if (!random)
return(list(entity = entity, stat = t))
else return(stat = t)
}
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.