queryOC: single-variant query

Description Usage Arguments Note Examples

View source: R/query.R

Description

single-variant query

Usage

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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

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queryOC # don't want to use auth

vjcitn/oc2bioc documentation built on Jan. 31, 2021, 6:20 p.m.