queryOC.Rd
single-variant query
queryOC(
baseURL = "https://run.opencravat.org",
uname,
passwd,
chr = "chr1",
pos = "12777320",
ref = "G",
alt = "T",
annotators = c("clinvar", "dbsnp", "exac_gene", "go", "rvis")
)
character(1) URL for server to use
user name registered at run.opencravat.org; will use value of environment variable OCRAVAT_USERNAME if missing
password for opencravat account; will use value of environment variable OCRAVAT_PASSWORD if missing
character(1) chromosome in chrn format
character(1) position, in hg38 coordinates
character(1) reference base
character(1) alternate base
character() vector of annotator tags
The default value of `baseURL` entails that this function will query run.opencravat.org. A username and password must be supplied in this case. For other values of `baseURL`, no authentication is attempted at this time. For a local instance of OpenCRAVAT, `http://0.0.0.0:8080` is a default setting for baseURL.
queryOC # don't want to use auth
#> function (baseURL = "https://run.opencravat.org", uname, passwd,
#> chr = "chr1", pos = "12777320", ref = "G", alt = "T", annotators = c("clinvar",
#> "dbsnp", "exac_gene", "go", "rvis"))
#> {
#> if (baseURL == "https://run.opencravat.org") {
#> if (missing(uname))
#> uname = Sys.getenv("OCRAVAT_USERNAME")
#> if (missing(passwd))
#> passwd = Sys.getenv("OCRAVAT_PASSWORD")
#> if (nchar(uname) == 0)
#> stop("no username available and baseURL is run.opencravat.org")
#> loginOC(uname = uname, passwd = passwd)
#> on.exit(logoutOC())
#> }
#> q = paste0(baseURL, "/submit/annotate?", "chrom=", chr, "&pos=",
#> pos, "&ref_base=", ref, "&alt_base=", alt, "&annotators=",
#> paste(annotators, collapse = ","))
#> httr::GET(q)
#> }
#> <bytecode: 0x176114898>
#> <environment: namespace:oc2bioc>