# R/shrinkRM.R In wiscstatman/Rolemodel: Gene-set analysis via MFA

#### Documented in shrinkRM

```shrinkRM <- function(I, y, alpha, gamma, p){

## Check validity of arguments
if(p <= 0 | p >= 1)
stop('p should be between 0 and 1')
if(alpha <= 0 | alpha >= 1)
stop('alpha should be between 0 and 1')
if(gamma <= 0 | gamma >= 1)
stop('gamma should be between 0 and 1')
if(alpha > gamma)
stop('alpha should be less than gamma')
## Check the validity of I and y
if(!all(I %in% c(0,1)))
stop('I should only consisit of 0 and 1')
if(!all(y %in% c(0,1)))
stop('y should only consisit of 0 and 1')

c1 <- log(p) - log(1-p)
c2 <- log(1-gamma) - log(1-alpha)
c3 <- log(gamma) - log(alpha)
Wstar <- apply(X = I, MARGIN = 2, FUN = function(x) (c1+ sum(x*y)*c3) < 0)

if(sum(Wstar)==0)
{
newI <- I
newy <- y
}
else
{
if(sum(Wstar) == 1)
indict <- any(sapply(which(I[, Wstar] == 1), function(t) sum(I[t,]*Wstar) == sum(I[t,])))
else
indict <- apply(X = I[, Wstar], MARGIN = 2, FUN = function(x) any(sapply(which(x == 1), function(t) sum(I[t,]*Wstar) == sum(I[t,]))))
##if indict[i] is TRUE, then the GO term corresponding to i must be 0 in the optimal solution of ILP.
Wstar[Wstar] <- indict
W1 <- !Wstar
if(sum(W1)==0)
{
print('Attention: all wholes and parts are zeros (inactive) in the optiaml solution!') ### Errors will be reported if using stop().
return() ## NULL
}
if(sum(W1)==1)
{
newI <- as.matrix(I[,W1][I[,W1]>0])
colnames(newI) <- colnames(I)[W1]
newy <- y[I[,W1]>0]
}
if(sum(W1)>1)
{
P1 <- (apply(X = I[,W1], MARGIN = 1, FUN = sum) > 0)
newI <- I[P1, W1]
newy <- y[P1]
}
}
return(list(newI = newI, newy = newy))
}
```
wiscstatman/Rolemodel documentation built on May 28, 2017, 4:34 a.m.