#' run_the_tests()
#'
#' Runs the specified enrichment test(s) and returns a table of results
#'
#' @param Output.miner list output from lipid.miner() function run on the Query dataset
#' @param Y has to be either a second output.miuner (e.g. Universe.miner) list output from lipid.miner() function run on the Universe dataset OR a RankingTable if the test is KS
#' @param test.type character string specifying the type of enrichment test. Valid values are: "Fisher", "Binom", "Hyper", "EASE", or "KS".
#' @param general.select vector of logical values of length ?, where the vector specifies ? in the following order ?
#' @param subset.by character string specifying one of "category", "mainclass", or "subclass", which denote the ?
#' @param subset.select vector of logical values of length ?, where the vector specifies ? in the following order ?
#' @param enrich logical value specifying whether to ?
#' @param p is a regular pvalue to use as a cutoff for the enrichment
#' @param q is a FDR qvalue adjusted using the bioconductor package qvalue
#'
#' @example run_the_tests(lipid.miner(cleaned.queryExample,output.list = T), lipid.miner(cleaned.universeExample,output.list = T), test.type="Fisher",general.select=c(T,T,T,T,T),subset.select=c(T,T,T),enrich=F,subset.by = "category")
#' @example run_the_tests(lipid.miner(cleaned.RTexample[,1],output.list = T), cleaned.RTexample, test.type="KS",general.select=c(T,T,T,T,T),subset.select=c(T,T,T),enrich=F,subset.by = "category")
#'
#' @author Geremy Clair, Kelly Stratton
#' @export
#'
run_the_tests <- function(X, Y, test.type, general.select, subset.by, subset.select, enrich, p, q, order="ascending"){
if(missing(order)){order="ascending"}
#verify that Query.miner is of the right type
if(test.type!="KS"){
if(!is.list(Y) & !names(Y)== c("intact","chain","allchains")){stop("Query.miner is of the wrong type")}
if(is.list(Y) & names(Y)== c("intact","chain","allchains")){
Universe.miner<-Y
} else{stop("Y seems to be a rankingTable, 'KS' is the only type of test working with such object")}
} else if(test.type=="KS"){
if(!is.null(names(Y))) {
if(all(names(Y) %in% c("intact","chain","allchains"))){
stop("Y is a an object generated with lipid.miner, 'KS' cannot be used as test")
} else {
rankingTable<-Y
}
}else{
stop("Improper ranking table")
}
}
#Fisher
if(test.type=="Fisher"){
#intact cat
if("cat" %in% general.select){
if (enrich==T){
intact_cat_result <- intact.fisher.enrich(X$intact$Category, Y$intact$Category,p=p,q=q)
}else{
intact_cat_result <- intact.fisher(X$intact$Category, Y$intact$Category)
}}
#intact main
if("main" %in% general.select){
if (enrich==T){
intact_main_result <- intact.fisher.enrich(X$intact$`Main class`, Y$intact$`Main class`,p=p,q=q)
}else{
intact_main_result <- intact.fisher(X$intact$`Main class`, Y$intact$`Main class`)
}}
#intact sub
if("sub" %in% general.select){
if (enrich==T){
intact_sub_result <- intact.fisher.enrich(X$intact$`Sub class`, Y$intact$`Sub class`,p=p,q=q)
}else{
intact_sub_result <- intact.fisher(X$intact$`Sub class`, Y$intact$`Sub class`)
}}
#chain
if("chains" %in% general.select){
if (enrich==T){
chain_result <- chain.fisher.enrich(X$chain, Y$chain,p=p,q=q)
}else{
chain_result <- chain.fisher(X$chain, Y$chain)
}}
#allchains
if("length" %in% general.select){
if (enrich==T){
allchains_result <- allchains.fisher.enrich(X$allchains, Y$allchains,p=p,q=q)
}else{
allchains_result <- allchains.fisher(X$allchains, Y$allchains)
}}
#sub total carbon
if("total_carbon" %in% subset.select){
if (subset.by=="category"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_carbon_result<- total.carbon.main(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_carbon_result<- total.carbon.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.main(X$intact,Y$intact, enrich=enrich,p=p,q=q))
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q))
}
}
#sub total DB
if("total_insaturation" %in% subset.select){
if (subset.by=="category"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_DB_result<- total.DB.main(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_DB_result<- total.DB.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.main(X$intact,Y$intact, enrich=enrich,p=p,q=q))
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q))
}
}
#sub allchains
if("specific_chains" %in% subset.select){
if (subset.by=="category"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_allchains_result<- allchains.main(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_allchains_result<- allchains.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, enrich=enrich,p=p,q=q)
sub_allchains_result<- rbind(sub_allchains_result,allchains.main(X$intact,Y$intact, enrich=enrich,p=p,q=q))
sub_allchains_result<- rbind(sub_allchains_result,allchains.sub(X$intact,Y$intact, enrich=enrich,p=p,q=q))
}
}
}
#Binom
if(test.type=="Binom"){
#intact cat
if("cat" %in% general.select){
if (enrich==T){
intact_cat_result <- intact.binom.enrich(X$intact$Category, Y$intact$Category,p=p,q=q)
}else{
intact_cat_result <- intact.binom(X$intact$Category, Y$intact$Category)
}}
#intact main
if("main" %in% general.select){
if (enrich==T){
intact_main_result <- intact.binom.enrich(X$intact$`Main class`, Y$intact$`Main class`,p=p,q=q)
}else{
intact_main_result <- intact.binom(X$intact$`Main class`, Y$intact$`Main class`)
}}
#intact sub
if("sub" %in% general.select){
if (enrich==T){
intact_sub_result <- intact.binom.enrich(X$intact$`Sub class`, Y$intact$`Sub class`,p=p,q=q)
}else{
intact_sub_result <- intact.binom(X$intact$`Sub class`, Y$intact$`Sub class`)
}}
#chain
if("chains" %in% general.select){
if (enrich==T){
chain_result <- chain.binom.enrich(X$chain, Y$chain,p=p,q=q)
}else{
chain_result <- chain.binom(X$chain, Y$chain)
}}
#allchains
if("length" %in% general.select){
if (enrich==T){
allchains_result <- allchains.binom.enrich(X$allchains, Y$allchains,p=p,q=q)
}else{
allchains_result <- allchains.binom(X$allchains, Y$allchains)
}}
#sub total carbon
if("total_carbon" %in% subset.select){
if (subset.by=="category"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_carbon_result<- total.carbon.main(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_carbon_result<- total.carbon.sub(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "Binom", enrich=enrich,p=p,q=q)
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.main(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q))
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.sub(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q))
}
}
#sub total DB
if("total_insaturation" %in% subset.select){
if (subset.by=="category"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_DB_result<- total.DB.main(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_DB_result<- total.DB.sub(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "Binom", enrich=enrich,p=p,q=q)
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.main(X$intact,Y$intact, test= "Binom", enrich=enrich,p=p,q=q))
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.sub(X$intact,Y$intact, test= "Binom", enrich=enrich,p=p,q=q))
}
}
#sub allchains
if("specific_chains" %in% subset.select){
if (subset.by=="category"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_allchains_result<- allchains.main(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_allchains_result<- allchains.sub(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q)
sub_allchains_result<- rbind(sub_allchains_result,allchains.main(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q))
sub_allchains_result<- rbind(sub_allchains_result,allchains.sub(X$intact,Y$intact, test= "Binom",enrich=enrich,p=p,q=q))
}
}
}
#Hyper
if(test.type=="Hyper"){
#intact cat
if("cat" %in% general.select){
if (enrich==T){
intact_cat_result <- intact.hyper.enrich(X$intact$Category, Y$intact$Category,p=p,q=q)
}else{
intact_cat_result <- intact.hyper(X$intact$Category, Y$intact$Category)
}}
#intact main
if("main" %in% general.select){
if (enrich==T){
intact_main_result <- intact.hyper.enrich(X$intact$`Main class`, Y$intact$`Main class`,p=p,q=q)
}else{
intact_main_result <- intact.hyper(X$intact$`Main class`, Y$intact$`Main class`)
}}
#intact sub
if("sub" %in% general.select){
if (enrich==T){
intact_sub_result <- intact.hyper.enrich(X$intact$`Sub class`, Y$intact$`Sub class`,p=p,q=q)
}else{
intact_sub_result <- intact.hyper(X$intact$`Sub class`, Y$intact$`Sub class`)
}}
#chain
if("chains" %in% general.select){
if (enrich==T){
chain_result <- chain.hyper.enrich(X$chain, Y$chain,p=p,q=q)
}else{
chain_result <- chain.hyper(X$chain, Y$chain)
}}
#allchains
if("length" %in% general.select){
if (enrich==T){
allchains_result <- allchains.hyper.enrich(X$allchains, Y$allchains,p=p,q=q)
}else{
allchains_result <- allchains.hyper(X$allchains, Y$allchains)
}}
#sub total carbon
if("total_carbon" %in% subset.select){
if (subset.by=="category"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_carbon_result<- total.carbon.main(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_carbon_result<- total.carbon.sub(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "Hyper", enrich=enrich,p=p,q=q)
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.main(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q))
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.sub(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q))
}
}
#sub total DB
if("total_insaturation" %in% subset.select){
if (subset.by=="category"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_DB_result<- total.DB.main(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_DB_result<- total.DB.sub(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "Hyper", enrich=enrich,p=p,q=q)
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.main(X$intact,Y$intact, test= "Hyper", enrich=enrich,p=p,q=q))
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.sub(X$intact,Y$intact, test= "Hyper", enrich=enrich,p=p,q=q))
}
}
#sub allchains
if("specific_chains" %in% subset.select){
if (subset.by=="category"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_allchains_result<- allchains.main(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_allchains_result<- allchains.sub(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q)
sub_allchains_result<- rbind(sub_allchains_result,allchains.main(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q))
sub_allchains_result<- rbind(sub_allchains_result,allchains.sub(X$intact,Y$intact, test= "Hyper",enrich=enrich,p=p,q=q))
}
}
}
#EASE
if(test.type=="EASE"){
#intact cat
if("cat" %in% general.select){
if (enrich==T){
intact_cat_result <- intact.EASE.enrich(X$intact$Category, Y$intact$Category,p=p,q=q)
}else{
intact_cat_result <- intact.EASE(X$intact$Category, Y$intact$Category)
}}
#intact main
if("main" %in% general.select){
if (enrich==T){
intact_main_result <- intact.EASE.enrich(X$intact$`Main class`, Y$intact$`Main class`,p=p,q=q)
}else{
intact_main_result <- intact.EASE(X$intact$`Main class`, Y$intact$`Main class`)
}}
#intact sub
if("sub" %in% general.select){
if (enrich==T){
intact_sub_result <- intact.EASE.enrich(X$intact$`Sub class`, Y$intact$`Sub class`,p=p,q=q)
}else{
intact_sub_result <- intact.EASE(X$intact$`Sub class`, Y$intact$`Sub class`)
}}
#chain
if("chains" %in% general.select){
if (enrich==T){
chain_result <- chain.EASE.enrich(X$chain, Y$chain,p=p,q=q)
}else{
chain_result <- chain.EASE(X$chain, Y$chain)
}}
#allchains
if("length" %in% general.select){
if (enrich==T){
allchains_result <- allchains.EASE.enrich(X$allchains, Y$allchains,p=p,q=q)
}else{
allchains_result <- allchains.EASE(X$allchains, Y$allchains)
}}
#sub total carbon
if("total_carbon" %in% subset.select){
if (subset.by=="category"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_carbon_result<- total.carbon.main(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_carbon_result<- total.carbon.sub(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_carbon_result<- total.carbon.cat(X$intact,Y$intact, test= "EASE", enrich=enrich,p=p,q=q)
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.main(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q))
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.sub(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q))
}
}
#sub total DB
if("total_insaturation" %in% subset.select){
if (subset.by=="category"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_total_DB_result<- total.DB.main(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_total_DB_result<- total.DB.sub(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_total_DB_result<- total.DB.cat(X$intact,Y$intact, test= "EASE", enrich=enrich,p=p,q=q)
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.main(X$intact,Y$intact, test= "EASE", enrich=enrich,p=p,q=q))
sub_total_DB_result<- rbind(sub_total_DB_result,total.DB.sub(X$intact,Y$intact, test= "EASE", enrich=enrich,p=p,q=q))
}
}
#sub allchains
if("specific_chains" %in% subset.select){
if (subset.by=="category"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="mainclass"){
sub_allchains_result<- allchains.main(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="subclass"){
sub_allchains_result<- allchains.sub(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
}
if (subset.by=="all"){
sub_allchains_result<- allchains.cat(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q)
sub_allchains_result<- rbind(sub_allchains_result,allchains.main(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q))
sub_allchains_result<- rbind(sub_allchains_result,allchains.sub(X$intact,Y$intact, test= "EASE",enrich=enrich,p=p,q=q))
}
}
}
#KS
if(test.type=="KS"){
#intact cat
if("cat" %in% general.select){
if (enrich==T){
intact_cat_result <- intact.KS.enrich(X$intact, colname= "Category", rankingTable , p=p , q=q , order=order)
}else{
intact_cat_result <- intact.KS(X$intact, colname= "Category", rankingTable , order=order)
}}
#intact main
if("main" %in% general.select){
if (enrich==T){
intact_main_result <- intact.KS.enrich(X$intact, colname= "Main class", rankingTable , p=p , q=q , order=order)
}else{
intact_main_result <- intact.KS(X$intact, colname= "Main class", rankingTable , order=order)
}}
#intact sub
if("sub" %in% general.select){
if (enrich==T){
intact_sub_result <- intact.KS.enrich(X$intact, colname= "Sub class", rankingTable , p=p , q=q , order=order)
}else{
intact_sub_result <- intact.KS(X$intact, colname= "Sub class", rankingTable , order=order)
}}
#chain
if("chains" %in% general.select){
if (enrich==T){
chain_result <- chain.KS.enrich(X$chain, rankingTable , p=p , q=q , order=order)
}else{
chain_result <- chain.KS(X$chain, rankingTable, order=order)
}}
#allchains
if("length" %in% general.select){
if (enrich==T){
allchains_result <- allchains.KS.enrich(X$allchains, rankingTable , p=p , q=q , order=order)
}else{
allchains_result <- allchains.KS(X$allchains, rankingTable , order=order)
}}
#sub total carbon
if("total_carbon" %in% subset.select){
if (subset.by=="category"){
sub_total_carbon_result<- total.carbon.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="mainclass"){
sub_total_carbon_result<- total.carbon.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="subclass"){
sub_total_carbon_result<- total.carbon.sub.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="all"){
sub_total_carbon_result<- total.carbon.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
sub_total_carbon_result<- rbind(sub_total_carbon_result, total.carbon.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
sub_total_carbon_result<- rbind(sub_total_carbon_result,total.carbon.sub.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
}
}
#sub total DB
if("total_insaturation" %in% subset.select){
if (subset.by=="category"){
sub_total_DB_result<- total.DB.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="mainclass"){
sub_total_DB_result<- total.DB.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="subclass"){
sub_total_DB_result<- total.DB.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="all"){
sub_total_DB_result <- total.DB.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
sub_total_DB_result <- rbind(sub_total_DB_result, total.DB.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
sub_total_DB_result <- rbind(sub_total_DB_result, total.DB.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
}
}
#sub allchains
if("specific_chains" %in% subset.select){
if (subset.by=="category"){
sub_allchains_result<- allchains.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="mainclass"){
sub_allchains_result<- allchains.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="subclass"){
sub_allchains_result<- allchains.sub.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
}
if (subset.by=="all"){
sub_allchains_result <- allchains.cat.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q)
sub_allchains_result <- rbind(sub_allchains_result, allchains.main.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
sub_allchains_result <- rbind(sub_allchains_result, allchains.sub.KS(X$intact , rankingTable , order = order , enrich=enrich , p=p , q=q))
}
}
}
#Output tables if the corresponding object is not NA
#section titles object
title.enrich<-NA
#create a global output object (for a global download of the results)
if(test.type=="KS"){
global.output<-data.frame(matrix(nrow=0,ncol=5))
colnames(global.output)<-c("Test.performed","Classifier","Count.in.list", "p-value", "FDR.q-value")
} else {
global.output<-data.frame(matrix(nrow=0,ncol=9))
colnames(global.output)<-c("Test.performed","Classifier","Count.query","Count.universe","%.query","%.universe","p-value", "FDR.q-value","Fold.change")
}
options(warn=-1)
if(exists("intact_cat_result")){
title.enrich<- paste("Category(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
intact_cat_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich,intact_cat_result))
}
if(exists("intact_main_result")){
title.enrich<- paste("Main class(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
intact_main_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich,intact_main_result))
}
if(exists("intact_sub_result")){
title.enrich<- paste("Sub class(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
intact_sub_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich,intact_sub_result))
}
if(exists("chain_result")){
title.enrich<- paste("Chain(s) characteristics(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
chain_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich,chain_result))
}
if(exists("allchains_result")){
title.enrich<- paste("Specific chain(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
allchains_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich,allchains_result))
}
if(exists("sub_total_carbon_result")){
title.enrich<- paste("Total chain carbon by ",subset.by,"(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
sub_total_carbon_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich, sub_total_carbon_result))
}
if(exists("sub_total_DB_result")){
title.enrich<- paste("Total number of DB by ",subset.by,"(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
sub_total_DB_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich, sub_total_DB_result))
}
if(exists("sub_allchains_result")){
title.enrich<- paste("Specific chains by ",subset.by,"(",test.type,")",sep="")
#display title
title.enrich
#display this on the right panel
sub_allchains_result
global.output<-rbind(global.output,cbind(Test.performed=title.enrich, sub_allchains_result))
}
# download the global output
return(global.output)
}
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