queryOC: single-variant query

In vjcitn/oc2bioc: simple interfaces from OpenCRAVAT to Bioconductor

Description

single-variant query

Usage

queryOC(
  baseURL = "https://run.opencravat.org",
  uname,
  passwd,
  chr = "chr1",
  pos = "12777320",
  ref = "G",
  alt = "T",
  annotators = c("clinvar", "dbsnp", "exac_gene", "go", "rvis")
)

Arguments

baseURL	character(1) URL for server to use
uname	user name registered at run.opencravat.org; will use value of environment variable OCRAVAT_USERNAME if missing
passwd	password for opencravat account; will use value of environment variable OCRAVAT_PASSWORD if missing
chr	character(1) chromosome in chrn format
pos	character(1) position, in hg38 coordinates
ref	character(1) reference base
alt	character(1) alternate base
annotators	character() vector of annotator tags

Note

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.

Examples

queryOC # don't want to use auth

vjcitn/oc2bioc documentation built on Aug. 11, 2021, 1:04 p.m.