### NOTE: The following libraries need to be loaded to run this: ### Biobase, GO, YEAST

GetDepthMat <- function(genes.list, gocategory, dataLib) {

###################################################### ### LOADING LIBRARIES ######################################################

require(Biobase) || stop("need Biobase") require(GO) || stop("need GO")

## Function that takes a GO probe ID and returns a vector of all ## BP terms annotated to it. getterms<-function(probe, gocat) { a<-get(probe, dataLib)

if(length(a) <= 1) { if (is.na(a)) { return(c("0")) } }

### Keep the GO annotations from the specific Ontology

a1 <- unlist(a) a1 <- as.vector(a1)

a2 <- a1[seq(1,length(a1),by=3)]

a2.cat <- a1[seq(3,length(a1),by=3)]

b <- a2[a2.cat == gocat]

if (gocat == "BP") { b <- b[b != "GO:0003673"] b <- b[b != "GO:0000004"] }

else if (gocat == "MF") { b <- b[b != "GO:0003673"] b <- b[b != "GO:0005554"]

}

else if (gocat == "CC") { b <- b[b != "GO:0003673"] b <- b[b != "GO:0008372"]

}

if (length(b) == 0){ return(c("0")) }

myvec <- c() for (i in 1: length(b)) { myvec <- c(myvec, b[i]) return.vec <- recurse.terms(b[i], myvec, gocat) myvec <- return.vec }

return(unique(myvec)) }

recurse.terms <- function(Node, Container, gocat) { if (gocat == "BP") { parents <- get(Node, GOBPPARENTS) }

else if (gocat == "MF") { parents <- get(Node, GOMFPARENTS) }

else if (gocat == "CC") { parents <- get(Node, GOCCPARENTS) }

if (parents[1] == "GO:0003673") { Container <- Container }

else { num.parents <- length(parents)

for (j in 1:num.parents) { Container <- c(Container, parents[j]) Container <- recurse.terms(parents[j], Container, gocat) } } return(Container) }

### Function that will return the MINIMUM distance to the root for each term

getdepth <- function(Node, gocat) { Count <- 0 Count.List <- c()

if (gocat == "BP") { parents <- get(Node, GOBPPARENTS) }

else if (gocat == "MF") { parents <- get(Node, GOMFPARENTS) }

else if (gocat == "CC") { parents <- get(Node, GOCCPARENTS) }

parents <- parents[parents != "GO:0003673"]

if (length(parents) == 0) { Count <- Count + 1 Count.List <- c(Count.List,Count) } else { num.parents <- length(parents) Count <- Count + 1

for (i in 1: num.parents) { Count.List <- c(Count.List, Count) Return.List <- Recurse.Depth(parents[i], Count.List, gocat) Count.List <- Return.List } } #return(Count.List) return(min(Count.List)) }

Recurse.Depth <- function(Node, Container, gocat) { Last <- length(Container) Current.Count <- Container[Last] Container <- Container[1:Last-1]

if (gocat == "BP") { parents <- get(Node, GOBPPARENTS) }

else if (gocat == "MF") { parents <- get(Node, GOMFPARENTS) }

else if (gocat == "CC") { parents <- get(Node, GOCCPARENTS) }

if (length(parents) == 1 & parents[1] == "GO:0003673") { Current.Count <- Current.Count + 1 Container <- c(Container, Current.Count) }

else { if(sum(parents == "GO:0003673") >0 ) { Container <- c(Container, rep(Current.Count+1, sum(parents == "GO:0003673"))) parents <- parents[!(parents == "GO:0003673")] }

num.parents <- length(parents)

if (num.parents > 0) { Current.Count <- Current.Count + 1

for (j in 1:num.parents) { Container <- c(Container, Current.Count) Return.List <- Recurse.Depth(parents[j], Container, gocat) Container <- Return.List } } } return(Container) }

### FUNCTION THAT WILL RETURN THE DEPTH OF A NODE USING DEPTH-MATRIX

find.depth <- function(Node, depth.mat) { index <- names(depth.mat) == Node depth <- depth.mat[index] return(depth) }

###################################################### ###### PROCESSING THE INPUT DATA ######################################################

terms1<-sapply(genes.list, getterms, gocat = gocategory)

### Remove all terms and corresponding genes with "0" annotations

lose <- terms1 == "0" terms1 <- terms1[!lose] genes.list1<-genes.list[!lose]

terms1.unique <- c() for (i in 1:length(terms1)) { terms1.unique <- c(terms1.unique, terms1[[i]]) }

terms1.unique <- unique(terms1.unique)

### Get the depth of each term

terms1.depth <- sapply(terms1.unique, getdepth, gocat = gocategory) names(terms1.depth) <- terms1.unique

### OBTAIN MATRIX OF DEPTH OF INTERSECTION OF PAIR OF GENES

depthmat <- matrix(0, length(genes.list1), length(genes.list1)) row.names(depthmat) <- genes.list1

for (i in 2:length(genes.list1)) {

for (j in 1:(i-1)) { set1 <- terms1[[i]] set2 <- terms1[[j]] keep <- which(set1 %in% set2) if (sum(keep) == 0) { depthmat[i,j] <- 0 } else { int.set <- set1[keep] int.set.depth <- sapply(int.set, find.depth, depth.mat = terms1.depth) depthmat[i,j] <- max(int.set.depth) } } }

#### RETURN MATRIX depthmat <- depthmat + t(depthmat) return(depthmat) }