haploR-regulomeSummary: This function queries RegulomeDB web-based tool and returns...

In haploR: Query 'HaploReg', 'RegulomeDB'

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.

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

Usage

regulomeSearch(
  query = NULL,
  genomeAssembly = NULL,
  limit = 1000,
  timeout = 100
)

regulomeSummary(
  query = NULL,
  limit = 1000,
  genomeAssembly = NULL,
  timeout = 100
)

Arguments

query	Query (a vector of rsIDs).
genomeAssembly	Genome assembly built: can be GRCh37 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 list with the following items: - guery_coordinates - features - regulome_score - variants - nearby_snps, - assembly

a data frame (table)

Examples

data <- regulomeSearch("rs4791078")
head(data)
data <- regulomeSummary(c("rs4791078","rs10048158"))
head(data)

haploR documentation built on Oct. 9, 2023, 5:09 p.m.