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#### Build the Biological process ontologies (Go tree) ###
#' Building tree one
#'
#' @param t The GO root term
#' @keywords internal
#'
#' @return returns GO terms
#'
#'
GOTermsApp.B <- function(t){
h <- 1
assign(t, h, envir = go2h)
terms <- xx.ch[[t]]
terms <- terms[!is.na(terms)]
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
assign(terms[i], h, envir = go2h)
}
}
flag <- 1
while(flag){
L <- length(terms)
if(L > 0){
terms <- all_terms_level_h2(xx.ch, terms)
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
f <- exists(terms[i], envir=go2h)
if(!f){
assign(terms[i], h, envir = go2h)
}else{
aux <- get(terms[i], envir = go2h)
aux <- c(aux, h)
assign(terms[i], aux, envir = go2h)
}
}
}
}else{
flag <- 0
}
}
}
####################################################
#' Title
#'
#' @param t The root GO term to build the GO tree
#' @keywords internal
#' @return Returns the GO tree for Molecular function
#'
GOTermsApp.M <- function(t){
h <- 1
assign(t, h, envir = go2h1)
terms <- xx.ch1[[t]]
terms <- terms[!is.na(terms)]
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
assign(terms[i], h, envir = go2h1)
}
}
flag <- 1
while(flag){
L <- length(terms)
if(L > 0){
terms <- all_terms_level_h2(xx.ch1, terms)
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
f <- exists(terms[i], envir=go2h1)
if(!f){
assign(terms[i], h, envir = go2h1)
}else{
aux <- get(terms[i], envir = go2h1)
aux <- c(aux, h)
assign(terms[i], aux, envir = go2h1)
}
}
}
}else{
flag <- 0
}
}
}
#### Build the Cellular Component Ontology (Go tree) ###
#' Title
#'
#' @param t The root GO term to build the GO tree
#' @keywords internal
#' @return Returns the GO tree for Cellular component
#'
GOTermsApp.C <- function(t){
h <- 1
assign(t, h, envir = go2h2)
terms <- xx.ch2[[t]]
terms <- terms[!is.na(terms)]
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
assign(terms[i], h, envir = go2h2)
}
}
flag <- 1
while(flag){
L <- length(terms)
if(L > 0){
terms <- all_terms_level_h2(xx.ch2, terms)
L <- length(terms)
if(L > 0){
h <- h + 1
for(i in 1:L){
f <- exists(terms[i], envir=go2h2)
if(!f){
assign(terms[i], h, envir = go2h2)
}else{
aux <- get(terms[i], envir = go2h2)
aux <- c(aux, h)
assign(terms[i], aux, envir = go2h2)
}
}
}
}else{
flag <- 0
}
}
}
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