gsclist[1:10]
signature<-strsplit(gene_list," ")
signature
names(signature)[1]
names(signature)[1]<-"user_signature"
signature
names(gsclist) <- sapply(gsclist, `[[`, 1)
gsclist
unique(signature())
unique(signature)
uniqueList <- unique(signature)
makeSet <- function(geneIds, n) {GeneSet(geneIds, geneIdType=SymbolIdentifier(), setName=n)}
gsclist <- mapply(makeSet, uniqueList[], names(gsclist))
gsc <- GeneSetCollection(gsclist)
gsc
signature<-strsplit(gene_list," ")
names(signature)[1]<-"user_signature"
uniqueList <- unique(signature)
signature<-strsplit(gene_list," ")
names(signature)[1]<-"user_signature"
uniqueList <- unique(signature)
makeSet <- function(geneIds, n) {GeneSet(geneIds, geneIdType=SymbolIdentifier(), setName=n)}
gsclist <- mapply(makeSet, uniqueList[], names(signature))
gsc <- GeneSetCollection(gsclist)
gsc
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp()
runApp('JNJ/GSVA App Git backup')
runApp()
runApp('JNJ/GSVA App Git backup')
gene_list
input$gene_list
input$gene_list
runApp('JNJ/GSVA App Git backup')
input$gene_list
input$gene_list
input$gene_list
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
ui <- fluidPage(
actionButton("add", "Add UI")
)
server <- function(input, output, session) {
observeEvent(input$add, {
insertUI(
selector = "#add",
where = "afterEnd",
ui = textInput(paste0("txt", input$add),
"Insert some text")
)
})
}
shinyApp(ui, server)
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('Imperial/GSVA_app')
runApp('JNJ/GSVA App Git backup')
signature
signature()
signature
unique(signature)
unique(signature)[[1]]
unique(signature[[1]])
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
uniqueList
names(signature)
uniqueList
length(uniqueList)
length(unique(uniqueList))
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
gsclist
GeneSetCollection(gsclist)
gsclist
gene_list
names(signature)[1]<-"user_signature"
signature
uniqueList <- unique(signature[[1]])
uniqueList
uniqueList[]
names(signature)
gsclist <- mapply(makeSet, uniqueList[], names(signature))
gsclist
gsc <- GeneSetCollection(gsclist)
uniqueList
uniqueList
names(signature)[1]<-"user_signature"
signature
names(signature)[1]<-"user_signature"
signature[[1]]
signature[[1]]<-unique(signature[[1]])
uniqueList <- unique(signature[[1]])
uniqueList
makeSet <- function(geneIds, n) {GeneSet(geneIds, geneIdType=SymbolIdentifier(), setName=n)}
gsclist <- mapply(makeSet, uniqueList[], names(signature))
gsclist
geneIds
makeSet
uniqueList[]
names(signature)
gsclist <- mapply(makeSet, uniqueList[], names(signature))
gsclist
gsclist
gsc <- GeneSetCollection(gsclist)
gsclist
gsc <- GeneSetCollection(gsclist)
gsclist
gsc <- GeneSetCollection(gsclist)
gsc
gsclist
gsclist
GeneSetCollection(gsclist)
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
shiny::runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
gene_list
signature<-strsplit(gene_list," ")
signature
signature[[1]]<-unique(signature[[1]])
class(signature)
length(signature)
length(signature[[1]])
signature[[1]]<-unique(signature[[1]])
signature[[1]]
names(signature)[1]<-"user_signature"
uniqueList <- lapply(gsclist, unique)
signature
names(signature)[1]<-"user_signature"
uniqueList <- lapply(signature, unique)
uniqueList
makeSet <- function(geneIds, n) {GeneSet(geneIds, geneIdType=SymbolIdentifier(), setName=n)}
gsclist <- mapply(makeSet, uniqueList[], names(signature))
gsclist
gsc <- GeneSetCollection(gsclist)
gsc
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
runApp('JNJ/GSVA App Git backup')
gsetInput()
match(geneIds(gsetInput()),rownames(input$dataset))
rownames(input$dataset)
input$dataset
exprsets[[input$dataset]]
rownames(exprsets[[input$dataset]])
hgu<-as.list(hgu133plus2SYMBOL)
hgu
hgu<-as.list(hgu133plus2ALIAS2PROBE)
hgu
exprsets.gene.symbols<-list()
exprsets.gene.symbols[[input$dataset]]<-names(hgu)
exprsets.gene.symbols
exprsets
hgu<-as.list(hgu133plus2SYMBOL)
hgu
match(rownames(exprsets[[1]]),names(hgu))
hgu133plus2()[match(rownames(exprsets[[1]]),names(hgu))]
as.character(hgu)[match(rownames(exprsets[[1]]),names(hgu))]
hgu<-as.list(hgu133plus2SYMBOL)
hgu
match(rownames(exprsets[[1]]),names(hgu))
hgu[match(rownames(exprsets[[1]]),names(hgu))]
as.character(hgu)[match(rownames(exprsets[[1]]),names(hgu))]
exprsets.gene.symbols<-list()
exprsets
exprsets.gene.symbols$GSE5058<-as.character(hgu)[match(rownames(exprsets[[1]]),names(hgu))]
exprsets.gene.symbols$GSE36221<-as.character(hgu)[match(rownames(exprsets[[2]]),names(hgu))]
exprsets.gene.symbols
exprsets[[2]]
as.list(hugene10sttranscriptclusterSYMBOL)
hgu<-as.list(hugene10sttranscriptclusterSYMBOL)
exprsets.gene.symbols$GSE36221<-as.character(hgu)[match(rownames(exprsets[[2]]),names(hgu))]
exprsets.gene.symbols
exprsets.gene.symbols[[2]]
setwd("C:\\Users\\user\\Documents\\JNJ\\GSVA App Git backup\\data")
dir()
save(exprsets.gene.symbols,file="exprsets.gene.symbols.r")
load("exprsets.gene.symbols.r")
runApp('~/JNJ/GSVA App Git backup')
setInput()
gsetInput()
geneIds(gsetInput())
match(geneIds(gsetInput()),rownames(exprsets.gene.symbols[[input$dataset]]))
exprsets.gene.symbols
exprsets.gene.symbols[[1]]
exprsets.gene.symbols[[input$dataset]]
geneIds(gsetInput())
unlist(geneIds(gsetInput()))
match(unlist(geneIds(gsetInput())),rownames(exprsets.gene.symbols[[input$dataset]]))
match(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])
is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])
is.element((geneIds(gsetInput()),exprsets.gene.symbols[[input$dataset]])
is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])
unlist(geneIds(gsetInput()))[is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]]]
is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])
unlist(geneIds(gsetInput()))
unlist(geneIds(gsetInput()))[[1]]
is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])
unlist(geneIds(gsetInput()))[is.element(unlist(geneIds(gsetInput())),exprsets.gene.symbols[[input$dataset]])]
is.element(geneIds(gsetInput())[[1]],exprsets.gene.symbols[[input$dataset]])
geneIds(gsetInput()))[[1]][is.element(geneIds(gsetInput())[[1]],exprsets.gene.symbols[[input$dataset]])]
is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])
geneIds(gsetInput()[[1]][is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
]
is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])
geneIds(gsetInput()[[1]])
geneIds(gsetInput()[[1]])[is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
geneIds(gsetInput()[[1]])[!is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
missing.genes
paste(missing.genes)
lapply(paste,missing.genes)
lapply(missing.genes,paste)
lapply(missing.genes[],paste)
paste(missing.genes,collapse = '')
paste(missing.genes,collapse = ' ')
paste('the following genes are not on the platform',missing.genes,collapse = ' ')
paste(missing.genes,collapse = ' ')
paste(paste(missing.genes,collapse = ' '))
paste('the following genes are not on the platform',paste(missing.genes,collapse = ' '))
paste('the following genes are not on the platform:\n',paste(missing.genes,collapse = ' '))
paste('the following genes are not on the platform: ',paste(missing.genes,collapse = ' '))
paste('the following genes are not on the platform: ',paste(missing.genes,collapse = ', '))
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
missing.genes
geneIds(gsetInput()[[1]])[!is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
geneIds(gsetInput()[[1]])[!is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
values$gene_list
strsplit
strsplit(values$gene_list)
values$gene_list
strsplit(values$gene_list)
values$gene_list
strsplit(values$gene_list," ")
input$datasets
input$dataset
exprsets.gene.symbols[[input$dataset]]
match(strsplit(values$gene_list," "),exprsets.gene.symbols[[input$dataset]])
strsplit(values$gene_list," ")
exprsets.gene.symbols[[input$dataset]]
strsplit(values$gene_list," ")
match(strsplit(values$gene_list," ")[[1]],exprsets.gene.symbols[[input$dataset]])
is.element(strsplit(values$gene_list," ")[[1]],exprsets.gene.symbols[[input$dataset]])
sum(is.element(strsplit(values$gene_list," ")[[1]],exprsets.gene.symbols[[input$dataset]]))
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
geneIds(gsetInput()[[1]])[!is.element(geneIds(gsetInput()[[1]]),exprsets.gene.symbols[[input$dataset]])]
if(sum(is.element(strsplit(values$gene_list," ")[[1]],exprsets.gene.symbols[[input$dataset]]))==0) return(NULL)
sum(is.element(strsplit(values$gene_list," ")[[1]],exprsets.gene.symbols[[input$dataset]]))==0
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
exprsets$GSE5058
pd<-pData(exprsets$GSE5058)
pd$Age
pd$Gender
pd$Gender[pd$Gender=="Sex: M"]
pd$Gender[pd$Gender=="Sex: M"]="Male"
x<-pd$Gender
x<-as.character(pd$Gender)
as.character(x)
x
pd<-pData(exprsets$GSE5058)
pd$Gender
x<-as.character(pd$Gender)
x
x[x==Sex: M]
x[x=='Sex: M']
x[x=='Sex: M']="male"
unique(x)
x[x=='sex: M']="male"
x[x=="sex: F"]="female"
x[x=="Sex: F"]="female"
x
pd$Gender<-factor(x)
pd$Ethnicity
x<-as.character(pd$Ethnicity)
x
unique(x)
x[x=="Ethnic group: black"]="black"
x[x=="ethnic group: black"]="black"
x[x=="ethnic group: white"]="white"
x[x=="Ethnic group: hispanic"]="hispanic"
x[x=="ethnic group: hispanic"]="hispanic"
x[x=="Ethnic group: white"]="white"
pd$Ethnicity<-factor(x)
pData(exprsets$GSE5058)$Gender<-pd$Gender
pData(exprsets$GSE5058)$Ethnicity<-pd$Ethnicity
getwd()
save(exprsets,file="exprsets.r")
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
restable
res<-topTable(fit2, coef=1, adjust="BH", n=Inf)[,c('logFC','P.Value','adj.P.Val')]
colnames(res)[1]<-"Diff"
colnames(res)<-paste(rownames(restable)[1],colnames(res))
#limma does not return row name for a single signature, so need's to be checked and added
if (length(genesetnames)==1) rownames(res)<-genesetnames
res<-res[match(genesetnames,rownames(res)),]
if(length(comparisons)>1){
for (i in 2:length(comparisons)){
res2<-topTable(fit2, coef=i, adjust="BH", n=Inf)[,c('logFC','P.Value','adj.P.Val')]
colnames(res2)[1]<-"Diff"
colnames(res2)<-paste(rownames(restable)[i],colnames(res2))
if (length(genesetnames)==1) rownames(res2)<-genesetnames
res2<-res2[match(rownames(res),rownames(res2)),]
res<-cbind(res,res2)
}
}
# data.frame(t(res))
res
res
runApp('~/JNJ/GSVA App Git backup')
res<-run_limma(dat,genesetnames,input$cohort)
res
runApp('~/JNJ/GSVA App Git backup')
stats()
stats()
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
res
datatable(res)
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
input$significant
length(ind_sign)!=0
res
res
t(res)
res<-data.frame(t(res[ind_sign]))
res
cbind(rownames(res),res)
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
input$significant
length(ind_sign)
res
data.frame(t(res[ind_sign]))
class(res)
dim(res)
res
ind_sign
seq(3,ncol(res),3)
res[seq(3,ncol(res),3)]<0.05
res
res[1:3]
data.frame(t(res[ind_sign]))
res
res[ind_sign]
ind_sign
length(ind_sign)
length(ind_sign)/3
sort(ind_sign)
runApp('~/JNJ/GSVA App Git backup')
res
round(res,4)
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
datasetInput()[-grep("rownames\\(esdf\\)",names(datasetInput()))]
dim(datasetInput())
-grep("rownames\\(esdf\\)",names(datasetInput()))
runApp()
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
gene_list
regexpr
regexpr("\r\n",gene_list)
regexpr("\n",gene_list)
regexpr("\r?\n|\r",gene_list)
regexpr(" ",gene_list)
grep(" ",gene_list)
gene_list
unlist(gene_list)
strsplit(gene_list," ")
signature==""
signature<-strsplit(gene_list," ")
signature
signature[[1]]==""
signature()
signature
gene_list
Trim(clean(gene_list))
gsub("(?<=[\\s])\\s*|^\\s+|\\s+$", "", gene_list, perl=TRUE)
runApp('~/JNJ/GSVA App Git backup')
library(shiny)
runApp(list(
ui = pageWithSidebar(
headerPanel("'Reset inputs' button example"),
sidebarPanel(
uiOutput('resetable_input'),
tags$hr(),
actionButton("reset_input", "Reset inputs")
),
mainPanel(
h4("Summary"),
verbatimTextOutput("summary")
)
),
server = function(input, output, session) {
output$summary <- renderText({
return(paste(input$mytext, input$mynumber))
})
output$resetable_input <- renderUI({
times <- input$reset_input
div(id=letters[(times %% length(letters)) + 1],
numericInput("mynumber", "Enter a number", 20),
textInput("mytext", "Enter a text", "test"))
})
}
))
runApp('~/JNJ/GSVA App Git backup')
dat
datasetInput()
input$cohort
input$subset_cohort_2plot
dat <- datasetInput()[datasetInput()[[input$cohort]] %in% input$subset_cohort_2plot,]
dat
rownames(dat)<-dat[,1]
dat<-dat[,2:ncol(dat)]
dat
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
input$cohort
datasetInput()[[input$cohort]]
levels(datasetInput()[[input$cohort]])
length(levels(datasetInput()[[input$cohort]]))
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
myexprset
myexprset
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
res
round(res,4)
round(res,2)
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
runApp('~/JNJ/GSVA App Git backup')
