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#' This function queries HaploReg web-based tool
#' in order to Extended view for SNP of interest
#'
#' @param snp A SNP of interest.
#' @param url A url to HaploReg.
#' Default: <https://pubs.broadinstitute.org/mammals/haploreg/detail_v4.2.php?query=&id=>
#' @return A list of tables t1, t2, ..., etc
#' depending on information contained in HaploReg database.
#' @examples
#' tables <- getExtendedView(snp="rs10048158")
#' tables
#' @rdname haploR-getExtendedView
#' @export
getExtendedView <- function(snp, url=Haploreg.settings[["extended.view.url"]]) {
res <- list()
snp <- as.list(snp)
for(s in snp) {
# Construct a direct link:
ext.url <- paste(url, s, sep="")
# Get data:
page <- tryCatch(
{
xData <- getURL(ext.url)
htmlParse(xData)
}, error=function(e) {
if(url.exists(ext.url)) {
message(paste("URL does not seem to exist:", url))
}
message("Here's the original error message:")
message(e$message)
# Choose a return value in case of error
return(NULL)
}, warning=function(e) {
message(e$message)
# Choose a return value in case of warning
return(NULL)
}
)
if(is.null(page)) {
next
}
tables <- readHTMLTable(page)
#t1 <- readHTMLTable(page)[[1]]
tables[[1]] <- tables[[1]][-1,]
colnames(tables[[1]]) <- c("chr", "pos hg19", "chr2", "pos (hg38)", "Reference", "Alternate", "AFR", "AMR", "ASN", "EUR", "by GERP", "by SiPhy", "dbSNP functional annotation")
plain.names <- xpathSApply(page, "//p", xmlValue)
plain.names <- plain.names[plain.names != ""]
table.names <- c("Sequence facts",
"Closest annotated gene",
plain.names[4:length(plain.names)])
if (length(tables) >=2) {
#t2 <- readHTMLTable(page)[[2]]
colnames(tables[[2]]) <- as.character(unlist(c(tables[[2]][1,])))
tables[[2]] <- tables[[2]][-1,]
}
#table.names <- c(t.names, paste("t", 4:length(tables), sep=""))
names(tables) <- table.names
res[[s]] <- tables
}
return(res)
}
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