Nothing
output$outlierTable <- DT::renderDataTable({
inFile <- input$file1
file <- inFile$datapath
if (is.null(inFile)){
return(NULL)
}
sorted.snp <- sort(r.x()$x$pvalues, index.return = TRUE)
nna.idx <- which(!is.na(r.x()$x$pvalues))
nSNP <- length(r.x()$x$pvalues[nna.idx])
pc <- get.pc(r.x()$x, nna.idx[sorted.snp$ix])
if (is.null(r.ID()$inSNP)){
ID <- rep(NA, nSNP)
df <- data.frame(Rank = 1:nSNP, ID = ID, Index = sorted.snp$ix,
pvalue = sorted.snp$x, PC = pc[, 2])
} else {
ID <- read.table(r.ID()$inSNP$datapath, header = FALSE, stringsAsFactors = FALSE)[,1]
ID <- ID[nna.idx]
first.item <- ID[1]
letters <- strsplit(first.item, split = "")[[1]]
if (length(letters) > 2 && letters[1] == "r" && letters[2] == "s"){
ID.link <- paste0('<a href=https://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=', ID, ' target=_blank>', ID, '</a>')
df <- data.frame(Rank = 1:nSNP, ID = ID.link[sorted.snp$ix], Index = sorted.snp$ix,
pvalue = sorted.snp$x, PC = pc[, 2])
} else {
df <- data.frame(Rank = 1:nSNP, ID = ID[sorted.snp$ix], Index = sorted.snp$ix,
pvalue = sorted.snp$x, PC = pc[, 2])
}
}
dt <- DT::datatable(df, class = 'cell-border stripe',
rownames = FALSE,
escape = FALSE)
})
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