## Function for computing the ratio of between-groups to
## within-groups sum of squares.
##
## TAKEN FROM THE SMA PACKAGE (BIOCONDUCTOR).
# \references{S. Dudoit, J. Fridlyand, and T. P. Speed. Comparison of
# Discrimination Methods for the Classification of Tumors Using Gene
# Expression Data. June 2000. (Statistics, UC Berkeley,  Tech Report \#
# 576). } 
# 
# \author{
#   Sandrine Dudoit, \email{sandrine@stat.berkeley.edu}  \cr
#   Jane Fridlyand, \email{janef@stat.berkeley.edu}
# }

bwss<-function(x, cl)
 {
 # Compute BSS/WSS for each row of a matrix which may have NA
 # Columns have labels cl=consecutive integers
 
   K <- max(cl) - min(cl) + 1
   tvar <- apply(x, 1, var.na)
   tn <- apply(!is.na(x), 1, sum)
   wvar <- matrix(0, nrow(x), K)
   wn <- matrix(0, nrow(x), K)
 
   for(i in (1:K)) {
     if(sum(cl == (i + min(cl) - 1)) == 1) {
       wvar[, i] <- 0
       wn[, i] <- 1
     }
     if(sum(cl == (i + min(cl) - 1)) > 1) {
       wvar[, i] <- apply(x[, cl == (i + min(cl) - 1)], 1, var.na)
       wn[, i] <- apply(!is.na(x[, cl == (i + min(cl) - 1)]), 1, sum)
     }
   }
 
   WSS <- apply(wvar * (wn - 1), 1, sum.na)
   TSS <- tvar * (tn - 1)
   BSS<- TSS - WSS
   BW <- BSS/WSS
 
   list(wn=wn,bw=BW,bss=BSS,wss=WSS,tss=TSS,tvar=tvar)
 }
 
## Other functions taken from the same SMA package.
 mean.na <- function(x,...)
{
        mean(x[!(is.na(x) | is.infinite(x))])
}
 
 var.na <- function(x)
{
        res <- NA
        tmp <- !(is.na(x) | is.infinite(x))
        if(sum(tmp) > 1)
                res <- var(x[tmp])
        res
}

cor.na <- function(x)
{
  cor(x, use="pairwise.complete.obs")
}

sum.na <- function(x,...)
{
        res <- NA
        tmp <- !(is.na(x) | is.infinite(x))
        if(sum(tmp) > 0)
                res <- sum(x[tmp])
        res
}


length.na <- function(x, ...)
{
   tmp <- !(is.na(x) | is.infinite(x))
   length(x[tmp],...)
 }

log.na <- function(x, ...)
{
  log(ifelse(x > 0, x, NA), ...)
}