queryRegulome {haploR}

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

Description

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

Usage

queryRegulome(
  query = NULL,
  genomeAssembly = "GRCh37",
  limit = 1000,
  timeout = 100
)

Arguments

query

Query (a vector of rsIDs or exact one query region in rsid or like "chr1:39492461-39492462").

genomeAssembly

Genome assembly built: can be GRCh37 (default) or GRCh38.

limit

It controls how many variants will be queried and returned for a large region. It can be a number (1000 by default) or "all". Please note that large number or "all" may get yourself hurt because you could get timeout or may even crash the server.

timeout

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

Value

a data frame (table) OR a list with the following items: - guery_coordinates - features - regulome_score - variants - nearby_snps, - assembly

Examples

data <- queryRegulome(c("rs4791078","rs10048158"))
head(data)