haploR-queryRegulome: This function queries RegulomeDB <URL: www.regulomedb.org>...

Description Usage Arguments Value Examples

Description

This function queries RegulomeDB www.regulomedb.org web-based tool and returns results in a data frame.

Usage

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queryRegulome(query = NULL, format = "full",
  url = "http://www.regulomedb.org/results", timeout = 100,
  check_bad_snps = TRUE, verbose = FALSE)

Arguments

query

Query (a vector of rsIDs).

format

An output format. Can be on of the following: full - plain text, bed - BED (Browser Extensible Data) format, see e.g. <https://genome.ucsc.edu/FAQ/FAQformat.html#format5.1>, gff - GFF (General Feature Format), see e.g. <https://genome.ucsc.edu/FAQ/FAQformat.html#format3> Only full is currently supported.

url

Regulome url address. Default: <http://www.regulomedb.org/results>

timeout

A timeout parameter for httr::POST. Default: 100

check_bad_snps

Checks if all SNPs are annotated. Default: TRUE

verbose

Verbosing output. Default: FALSE.

Value

A list of two: (1) a data frame (table) and (2) a list of bad SNP IDs. Bad SNP ID are those IDs that were not found in 1000 Genomes Phase 1 data

Examples

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data <- queryRegulome(c("rs4791078","rs10048158"))
head(data[["res.table"]])
head(data[["bad.snp.id"]])

Example output

<simpleError in curl::curl_fetch_memory(url, handle = handle): Could not resolve host: archive.broadinstitute.org>
<simpleError in `[.data.frame`(res.table, , i): undefined columns selected>
# A tibble: 0 x 0
NULL

haploR documentation built on Jan. 19, 2019, 5:08 p.m.