Nothing
R/JumpNode.R
In GOxploreR: Structural Exploration of the Gene Ontology (GO) Knowledge Base
Defines functions
Level2JumpNodeCC
Level2JumpNodeMF
Level2JumpNodeBP
Documented in
Level2JumpNodeBP
Level2JumpNodeCC
Level2JumpNodeMF
#' Jump nodes from a GO BP level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least
#' one child term not present in the level below it. If the optional parameter "organism" is missing then
#' the results are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes from level 3
#' Level2JumpNodeBP(level = 3, organism = "Homo sapiens")
#'
#' # Jump nodes from level 6
#' Level2JumpNodeBP(level = 6, organism = "Arabidopsis thaliana")
#'
Level2JumpNodeBP <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralbp$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralbp$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO BP tree, the highest level is", 19 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- BPHuman$df[x,][1]
if(nonLeafNode != 0){
return(BPHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO BP tree, the highest level is", length(BPHuman$df[,1]) - 1 , sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::BPRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::BPRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::BPRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::BPMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::BPMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::BPMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- BPZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(BPZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(BPZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- BPElegan$df[x,][1]
if(nonLeafNode != 0){
return(BPElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(BPElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- BPTair$df[x,][1]
if(nonLeafNode != 0){
return(BPTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(BPTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- BPYeast$df[x,][1]
if(nonLeafNode != 0){
return(BPYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(BPYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- BPPombe$df[x,][1]
if(nonLeafNode != 0){
return(BPPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(BPPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- BPDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(BPDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(BPDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- BPEcoli$df[x,][1]
if(nonLeafNode != 0){
return(BPEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(BPEcoli$df[,1]) - 1, sep = " "))
})
}
}
#' Jump nodes from a GO MF level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have
#' at least one child term not present in the level below it. If the optional parameter "organism" is
#' missing then the results are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes on level 3
#' Level2JumpNodeMF(level = 3, organism = "Danio rerio" )
#'
#' # Jump nodes on level 6
#' Level2JumpNodeMF(level = 6, organism = "Caenorhabditis elegans" )
Level2JumpNodeMF <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralmf$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralmf$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO MF tree, the highest level is", 16 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- MFHuman$df[x,][1]
if(nonLeafNode != 0){
return(MFHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Human, the highest level is", length(MFHuman$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::MFRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::MFRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::MFRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::MFMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::MFMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::MFMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- MFZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(MFZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(MFZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- MFElegan$df[x,][1]
if(nonLeafNode != 0){
return(MFElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(MFElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- MFTair$df[x,][1]
if(nonLeafNode != 0){
return(MFTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(MFTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- MFYeast$df[x,][1]
if(nonLeafNode != 0){
return(MFYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(MFYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- MFPombe$df[x,][1]
if(nonLeafNode != 0){
return(MFPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(MFPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- MFDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(MFDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(MFDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- MFEcoli$df[x,][1]
if(nonLeafNode != 0){
return(MFEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(MFEcoli$df[,1]) - 1, sep = " "))
})
}
}
#' Jump nodes from a GO CC level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least
#' one child term not present in the level below it. If the optional parameter "organism" is missing then
#' the result are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes on level 5
#' Level2JumpNodeCC(level = 5, organism = "Saccharomyces cerevisiae" )
#'
#' # Jump nodes on level 3
#' Level2JumpNodeCC(level = 3, organism = "Schizosaccharomyces pombe" )
Level2JumpNodeCC <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralcc$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralcc$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO CC tree, the highest level is", 17 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- CCHuman$df[x,][1]
if(nonLeafNode != 0){
return(CCHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Human, the highest level is", length(CCHuman$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::CCRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::CCRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::CCRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::CCMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::CCMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::CCMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- CCZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(CCZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(CCZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- CCElegan$df[x,][1]
if(nonLeafNode != 0){
return(CCElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(CCElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- CCTair$df[x,][1]
if(nonLeafNode != 0){
return(CCTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(CCTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- CCYeast$df[x,][1]
if(nonLeafNode != 0){
return(CCYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(CCYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- CCPombe$df[x,][1]
if(nonLeafNode != 0){
return(CCPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(CCPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- CCDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(CCDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(CCDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- CCEcoli$df[x,][1]
if(nonLeafNode != 0){
return(CCEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(CCEcoli$df[,1]) - 1, sep = " "))
})
}
}
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Defines functions Level2JumpNodeCC Level2JumpNodeMF Level2JumpNodeBP
Documented in Level2JumpNodeBP Level2JumpNodeCC Level2JumpNodeMF
#' Jump nodes from a GO BP level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least
#' one child term not present in the level below it. If the optional parameter "organism" is missing then
#' the results are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes from level 3
#' Level2JumpNodeBP(level = 3, organism = "Homo sapiens")
#'
#' # Jump nodes from level 6
#' Level2JumpNodeBP(level = 6, organism = "Arabidopsis thaliana")
#'
Level2JumpNodeBP <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralbp$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralbp$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO BP tree, the highest level is", 19 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- BPHuman$df[x,][1]
if(nonLeafNode != 0){
return(BPHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO BP tree, the highest level is", length(BPHuman$df[,1]) - 1 , sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::BPRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::BPRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::BPRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::BPMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::BPMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::BPMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- BPZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(BPZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(BPZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- BPElegan$df[x,][1]
if(nonLeafNode != 0){
return(BPElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(BPElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- BPTair$df[x,][1]
if(nonLeafNode != 0){
return(BPTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(BPTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- BPYeast$df[x,][1]
if(nonLeafNode != 0){
return(BPYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(BPYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- BPPombe$df[x,][1]
if(nonLeafNode != 0){
return(BPPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(BPPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- BPDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(BPDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(BPDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- BPEcoli$df[x,][1]
if(nonLeafNode != 0){
return(BPEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(BPEcoli$df[,1]) - 1, sep = " "))
})
}
}
#' Jump nodes from a GO MF level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have
#' at least one child term not present in the level below it. If the optional parameter "organism" is
#' missing then the results are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes on level 3
#' Level2JumpNodeMF(level = 3, organism = "Danio rerio" )
#'
#' # Jump nodes on level 6
#' Level2JumpNodeMF(level = 6, organism = "Caenorhabditis elegans" )
Level2JumpNodeMF <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralmf$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralmf$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO MF tree, the highest level is", 16 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- MFHuman$df[x,][1]
if(nonLeafNode != 0){
return(MFHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Human, the highest level is", length(MFHuman$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::MFRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::MFRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::MFRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::MFMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::MFMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::MFMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- MFZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(MFZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(MFZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- MFElegan$df[x,][1]
if(nonLeafNode != 0){
return(MFElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(MFElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- MFTair$df[x,][1]
if(nonLeafNode != 0){
return(MFTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(MFTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- MFYeast$df[x,][1]
if(nonLeafNode != 0){
return(MFYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(MFYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- MFPombe$df[x,][1]
if(nonLeafNode != 0){
return(MFPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(MFPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- MFDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(MFDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(MFDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- MFEcoli$df[x,][1]
if(nonLeafNode != 0){
return(MFEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(MFEcoli$df[,1]) - 1, sep = " "))
})
}
}
#' Jump nodes from a GO CC level
#'
#' @param level A numeric value for the GO-level
#' @param organism Organism of interest that is supported by the package
#'
#' @description The function retrieves the Jump nodes (JNs) from a GO-level. JNs are those GO-terms which have at least
#' one child term not present in the level below it. If the optional parameter "organism" is missing then
#' the result are from the general GO tree. The supported organisms are "Homo sapiens / Human",
#' "Rattus norvegicus / Rat", "Mus musculus / Mouse", "Danio rerio / Zebrafish",
#' "Caenorhabditis elegans / Worm" ,"Arabidopsis thaliana / Cress", "Saccharomyces cerevisiae / Yeast",
#' "Schizosaccharomyces pombe / Fission yeast",
#' "Drosophila melanogaster / Fruit fly", "Escherichia coli / E.coli".
#'
#' @return All jump nodes from the level
#' @export
#' @import gontr
#' @examples
#' # Jump nodes on level 5
#' Level2JumpNodeCC(level = 5, organism = "Saccharomyces cerevisiae" )
#'
#' # Jump nodes on level 3
#' Level2JumpNodeCC(level = 3, organism = "Schizosaccharomyces pombe" )
Level2JumpNodeCC <- function(level, organism = NULL){
Organism <- organism
if(is.null(level) || !is.numeric(level)){
stop("The argument \"level\" is missing with no default or is non numeric")
}
x <- level + 1
if(!is.null(Organism) && !(toupper(Organism) %in% SupportedOrganism)){
print(SupportedOrganismv2)
stop("The \"organism\" argument should be given from the list above")
}
if(is.null(Organism)){
tryCatch({
nonLeafNode <- GOgeneralcc$df[x,][1]
if(nonLeafNode != 0){
return(GOgeneralcc$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for the General GO CC tree, the highest level is", 17 , sep = " "))
})
}else if(toupper(Organism) == "HOMO SAPIENS" || toupper(Organism) == "HUMAN"){
tryCatch({
nonLeafNode <- CCHuman$df[x,][1]
if(nonLeafNode != 0){
return(CCHuman$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Human, the highest level is", length(CCHuman$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "RATTUS NORVEGICUS" || toupper(Organism) == "RAT"){
tryCatch({
nonLeafNode <- gontr::CCRat$df[x,][1]
if(nonLeafNode != 0){
return(gontr::CCRat$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Rat, the highest level is", length(gontr::CCRat$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "MUS MUSCULUS" || toupper(Organism) == "MOUSE"){
tryCatch({
nonLeafNode <- gontr::CCMouse$df[x,][1]
if(nonLeafNode != 0){
return(gontr::CCMouse$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Mouse, the highest level is", length(gontr::CCMouse$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "DANIO RERIO" || toupper(Organism) == "ZEBRAFISH"){
tryCatch({
nonLeafNode <- CCZebrafish$df[x,][1]
if(nonLeafNode != 0){
return(CCZebrafish$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Zebrafish, the highest level is", length(CCZebrafish$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "CAENORHABDITIS ELEGANS" || toupper(Organism) == "WORM"){
tryCatch({
nonLeafNode <- CCElegan$df[x,][1]
if(nonLeafNode != 0){
return(CCElegan$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Caenorhabditis elegans, the highest level is", length(CCElegan$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ARABIDOPSIS THALIANA" || toupper(Organism) == "CRESS"){
tryCatch({
nonLeafNode <- CCTair$df[x,][1]
if(nonLeafNode != 0){
return(CCTair$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Arabidopsis thaliana, the highest level is", length(CCTair$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SACCHAROMYCES CEREVISIAE" || toupper(Organism) == "YEAST"){
tryCatch({
nonLeafNode <- CCYeast$df[x,][1]
if(nonLeafNode != 0){
return(CCYeast$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Saccharomyces cerevisiae, the highest level is", length(CCYeast$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "SCHIZOSACCHAROMYCES POMBE" || toupper(Organism) == "FISSION YEAST"){
tryCatch({
nonLeafNode <- CCPombe$df[x,][1]
if(nonLeafNode != 0){
return(CCPombe$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Schizosaccharomyces pombe, the highest level is", length(CCPombe$df[,1]) - 1, sep = " "))
})
}
else if(toupper(Organism) == "DROSOPHILA MELANOGASTER" || toupper(Organism) == "FRUIT FLY"){
tryCatch({
nonLeafNode <- CCDrosophila$df[x,][1]
if(nonLeafNode != 0){
return(CCDrosophila$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Drosophila melanogaster, the highest level is", length(CCDrosophila$df[,1]) - 1, sep = " "))
})
}else if(toupper(Organism) == "ESCHERICHIA COLI" || toupper(Organism) == "E.COLI"){
tryCatch({
nonLeafNode <- CCEcoli$df[x,][1]
if(nonLeafNode != 0){
return(CCEcoli$v[[as.character(nonLeafNode)]])
}
else{
return(NULL)
}
}, error = function(e){
print(paste("No such level exist for Escherichia coli, the highest level is", length(CCEcoli$df[,1]) - 1, sep = " "))
})
}
}
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