Nothing
gsta_gobp<-function(h,...){
gsta_goBP_params<-function(h,h2,h3,h4,h5,h6,h7,...){
run_params<-function(h,h2,h3,h4,h5,h6,h7,h8,h9,...){
ts_name=h;ts_val=h2;ann_pk<-h3;db<-h4;stat_sig<-h5;ctls<-h6;tsts<-h7;children=h8;r_choice=h9;
pb_ma<-tkProgressBar(title="GSTA GO Biological Process...",label="",min=0,max=1,initial=0.1,width=500)
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
test.goBP<-gtGO(groups,t(stat_sig[,samp_gsta]),annotation=db,ontology="BP",sort=TRUE)
res<-result(test.goBP)
names(res)[7]<-"Cov"
res1<-res[which(res$Cov!=0),]
res2<-res1
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
for(i in 1:dim(res1)[1])
{
x<-c()
for(j in 1:length(subsets(test.goBP)[[rownames(res1)[i]]]))
{
x<-paste(subsets(test.goBP)[[rownames(res1)[i]]][j],x,sep=",")
}
res2$genes[i]<-x
}
res2<-res2[,-1]
if(dim(res2)[1]==0)tkmessageBox(title="Warning",message="No results met the specified criteria",icon="warning",type="ok")
setTkProgressBar(pb_ma,0.8,title=NULL,label="")
gsta_gobp<-tclArray()
for(i in 0:dim(res2)[1]){ for(j in 0:dim(res2)[2]){
if(i==0){ gsta_gobp[[i,j]]<-colnames(res2)[j] } else {
if(j==0){ gsta_gobp[[i,j]]<-rownames(res2)[i] } else {
tem<-res2[i,j]
gsta_gobp[[i,j]]<-ifelse(is.na(tem),".",ifelse(is.numeric(tem),round(tem,digits=5),as.character(tem)))
} }
} }
setTkProgressBar(pb_ma,1,title="Completed...",label="")
close(pb_ma)
if(ts_name=="Affymetrix"){
GOtable.outBP_Affy[[ts_val]]<<-res2
ta_affy_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Agilent-OneColor"){
GOtable.outBP_Ag1[[ts_val]]<<-res2
ta_ag1_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Agilent-TwoColor"){
GOtable.outBP_Ag2[[ts_val]]<<-res2
ta_ag2_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Illumina-Beadarray"){
GOtable.outBP_Il_B[[ts_val]]<<-res2
ta_ilb_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Illumina-Lumi"){
GOtable.outBP_Il_L[[ts_val]]<<-res2
ta_ill_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Nimblegen"){
GOtable.outBP_N[[ts_val]]<<-res2
ta_nbl_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Series-Matrix"){
GOtable.outBP_S[[ts_val]]<<-res2
ta_smt_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
if(ts_name=="Online-Data"){
GOtable.outBP_O[[ts_val]]<<-res2
ta_onl_gsta_gobp[[ts_val]]<<-gsta_gobp
for(i in 1:length(children)){
x<-as.character(tcl(treeview,"item",children[i],"-values"))
if(x==r_choice[1]){p_enter_class<-tcl(treeview,"insert",children[i],"end",values=as.tclObj("...GSTA_GOBP"))}
}
}
}
ts_name=h;ts_val=h2;pre_rs=h3;samp_gsta=h4;groups=h5;children=h6;r_choice=h7;
if(ts_name=="Affymetrix"){
anAffy<-ann_Affy[[ts_val]]
if(length(grep("GPL[0-9]",anAffy))==0){
ann_pk<-anAffy
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anAffy),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_Affy[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anAffy,db,dat2Affy.m2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Agilent-OneColor"){
anAg1<-ann_Ag1[[ts_val]]
if(length(grep("GPL[0-9]",anAg1))==0){
ann_pk<-anAg1
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anAg1),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_Ag1[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anAg1,db,DE_Ag1_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Agilent-TwoColor"){
anAg2<-ann_Ag2[[ts_val]]
if(length(grep("GPL[0-9]",anAg2))==0){
ann_pk<-anAg2
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anAg2),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_Ag2[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anAg2,db,DE_Ag2_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Illumina-Beadarray"){
anIl_B<-ann_Il_B[[ts_val]]
if(length(grep("GPL[0-9]",anIl_B))==0){
ann_pk<-anIl_B
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anIl_B),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_Il_B[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anIl_B,db,DE_Il_B_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Illumina-Lumi"){
anIl_L<-ann_Il_L[[ts_val]]
if(length(grep("GPL[0-9]",anIl_L))==0){
ann_pk<-anIl_L
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anIl_L),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_Il_L[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anIl_L,db,DE_Il_L_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Nimblegen"){
anNbl<-ann_N[[ts_val]]
if(length(grep("GPL[0-9]",anNbl))==0){
ann_pk<-anNbl
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anNbl),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_N[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anNbl,db,DE_N_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Series-Matrix"){
anSmt<-ann_S[[ts_val]]
if(length(grep("GPL[0-9]",anSmt))==0){
ann_pk<-anSmt
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anSmt),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_S[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anSmt,db,DE_S_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
if(ts_name=="Online-Data"){
anOnl<-ann_O[[ts_val]]
if(length(grep("GPL[0-9]",anOnl))==0){
ann_pk<-anOnl
} else {
ann_pk<-pre_rs[which(pre_rs[,1]==anOnl),2]
if(length(ann_pk)==0){
tkmessageBox(title="Error",message="Annotation package not available for this platform",icon="warning",type="ok")
} else {
ann_O[[ts_val]]<<-ann_pk
}
}
if(ann_pk!=""){
db<-annPkgName(ann_pk)
if(!requireNamespace(db,quietly=TRUE)){
BiocManager::install(db,ask=FALSE,update=FALSE)
} else {
library(db,character.only=TRUE)
}
run_params(ts_name,ts_val,anOnl,db,DE_O_2[[ts_val]],samp_gsta,groups,children,r_choice)
}
}
}
r_choice="._."
children<-as.character(tcl(treeview,"children",""))
w_analz<-tktoplevel()
w_analz_frame<-ttkframe(w_analz,padding=c(3,3,50,20),borderwidth=1,relief="groove")
tkpack(w_analz_frame,expand=TRUE,fill="both",side="left")
var<-tclVar(tree_prnts[1])
sapply(tree_prnts,function(i){
r_but_vals<-ttkradiobutton(w_analz_frame,variable=var,text=i,value=i)
tkpack(r_but_vals,side="top",anchor="w")
})
tkpack(ttklabel(w_analz_frame,text=''))
tkpack(ttklabel(w_analz_frame,text=''))
r_but<-ttkbutton(w_analz_frame,text="Ok")
tkpack(r_but,pady=2)
tkconfigure(r_but,command=function(){
r_choice<-tclvalue(var)
tkwm.withdraw(w_analz)
tree_slc<-strsplit(r_choice[1],"_")
ts_name<-tree_slc[[1]][1]
ts_val<-as.numeric(tree_slc[[1]][2])
w_imp<-tktoplevel()
tkwm.title(w_imp,"Select Samples")
tkwm.resizable(w_imp,0,0)
frame_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
tkpack(ttklabel(frame_imp,text='Control Samples'),side="left",padx=45)
tkpack(ttklabel(frame_imp,text='Test Samples'),side="right",padx=62)
tkpack(frame_imp,expand=TRUE,fill="both",side="top")
frame2_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
controls<-tclVar("")
tkpack(ttkentry(frame2_imp,textvariable=controls,width=25),side="left",anchor="e")
tests<-tclVar("")
tkpack(ttkentry(frame2_imp,textvariable=tests,width=25),side="right",anchor="e")
tkpack(frame2_imp,expand=TRUE,fill="both",side="top")
frame3_imp<-ttkframe(w_imp,padding=c(3,3,12,12))
r_but<-ttkbutton(frame3_imp,text="Ok")
tkpack(r_but,side="right",padx=12)
tkpack(frame3_imp,expand=TRUE,fill="both",side="top")
tkconfigure(r_but,command=function(){
tkwm.withdraw(w_imp)
ctls<-tclvalue(controls);tsts<-tclvalue(tests);
xf<-strsplit(ctls,",")
yf<-strsplit(tsts,",")
samp_gsta<-c(xf[[1]],yf[[1]])
groups<-c(rep(0,length(xf[[1]])),rep(1,length(yf[[1]])))
err<-try({
if(!file.exists("GEOmetadb.sqlite")){
sqlfile<-getSQLiteFile(destdir=cur_dir,destfile="GEOmetadb.sqlite.gz",type="normal")
} else {
sqlfile<-"GEOmetadb.sqlite"
}
con<-dbConnect(SQLite(),sqlfile)
geo_tables<-dbListTables(con)
rs<-dbGetQuery(con,'select gpl,bioc_package from gpl')
rs2<-rs[!is.na(rs$bioc_package),]
rs3<-rs2[!(rs2$bioc_package==""),]
pre_rs<-rs3
},silent=TRUE)
if(length(grep("Error",err))!=0)
{
rs<-c("GPL71","GPL198","GPL2112","GPL3979","GPL3738","GPL200","GPL3213","GPL72","GPL1322","GPL199",
"GPL3154","GPL74","GPL201","GPL96","GPL571","GPL97","GPL14877","GPL570","GPL13667","GPL8300",
"GPL91","GPL92","GPL93","GPL94","GPL95","GPL887","GPL1708","GPL13497","GPL17897","GPL3921",
"GPL15396","GPL80","GPL5188","GPL17556","GPL6244","GPL11532","GPL18190","GPL8490","GPL13534","GPL6102",
"GPL6947","GPL10558","GPL32","GPL81","GPL33","GPL82","GPL34","GPL83","GPL339","GPL6246",
"GPL340","GPL1261","GPL8321","GPL75","GPL76","GPL3533","GPL341","GPL342","GPL1355","GPL85",
"GPL86","GPL87","GPL88","GPL1352","GPL1318","GPL2529","GPL90","GPL1319",
"ag","ath1121501","bovine","canine","canine2","celegans","chicken","drosgenome1","drosophila2","ecoli2",
"ecoli2","hcg110","hgfocus","hgu133a","hgu133a2","hgu133b","hgu133plus2","hgu133plus2","hgu219","hgu95av2",
"hgu95av2","hgu95b","hgu95c","hgu95d","hgu95e","hgug4110b","hgug4112a","HsAgilentDesign026652","hthgu133a","hthgu133a",
"hthgu133b","hu6800","huex10sttranscriptcluster","hugene10sttranscriptcluster","hugene10sttranscriptcluster",
"hugene11sttranscriptcluster","hugene11sttranscriptcluster","IlluminaHumanMethylation27k","IlluminaHumanMethylation450k","illuminaHumanv2",
"illuminaHumanv3","illuminaHumanv4","mgu74a","mgu74av2","mgu74b","mgu74bv2","mgu74c","mgu74cv2","moe430a","mogene10sttranscriptcluster",
"mouse4302","mouse430a2","mouse430a2","mu11ksuba","mu11ksubb","porcine","rae230a","rae230b","rat2302","rgu34a",
"rgu34b","rgu34c","rnu34","u133x3p","xenopuslaevis","yeast2","ygs98","zebrafish")
rs2<-matrix(rs,ncol=2)
colnames(rs2)<-c("gpl","bioc_package")
pre_rs<-data.frame(rs2)
}
gsta_goBP_params(ts_name,ts_val,pre_rs,samp_gsta,groups,children,r_choice)
})
})
}
pb_ma<-tkProgressBar(title="Loading packages...",label="",min=0,max=1,initial=0,width=500)
setTkProgressBar(pb_ma,0.1,title=NULL,label="")
if(!requireNamespace("gWidgets2tcltk",quietly=TRUE)){install.packages("gWidgets2tcltk");library(gWidgets2tcltk)} else {library(gWidgets2tcltk)}
setTkProgressBar(pb_ma,0.2,title=NULL,label="")
if(!requireNamespace("tkrplot",quietly=TRUE)){install.packages("tkrplot");library(tkrplot)} else {library(tkrplot)}
setTkProgressBar(pb_ma,0.3,title=NULL,label="")
if(!requireNamespace("BiocManager",quietly=TRUE)){install.packages("BiocManager");library(BiocManager)} else {library(BiocManager)}
setTkProgressBar(pb_ma,0.4,title=NULL,label="")
if(!requireNamespace("annotate",quietly=TRUE)){BiocManager::install("annotate",ask=FALSE,update=FALSE);library(annotate)} else {library(annotate)}
setTkProgressBar(pb_ma,0.5,title=NULL,label="")
if(!requireNamespace("GEOmetadb",quietly=TRUE)){BiocManager::install("GEOmetadb",ask=FALSE,update=FALSE);library(GEOmetadb)} else {library(GEOmetadb)}
setTkProgressBar(pb_ma,0.6,title=NULL,label="")
if(!requireNamespace("globaltest",quietly=TRUE)){BiocManager::install("globaltest",ask=FALSE,update=FALSE);library(globaltest)} else {library(globaltest)}
setTkProgressBar(pb_ma,0.7,title=NULL,label="")
if(!requireNamespace("RSQLite",quietly=TRUE)){install.packages("RSQLite",ask=FALSE,update=FALSE);library(RSQLite)} else {library(RSQLite)}
setTkProgressBar(pb_ma,0.9,title=NULL,label="")
if(!requireNamespace("DBI",quietly=TRUE)){install.packages("DBI",ask=FALSE,update=FALSE);library(DBI)} else {library(DBI)}
setTkProgressBar(pb_ma,1,title="Done...",label="")
close(pb_ma)
gsta_gobp()
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.