haploR-queryHaploreg: This function queries HaploReg web-based tool and returns...

Description Usage Arguments Value Examples

Description

This function queries HaploReg web-based tool and returns results.

Usage

1
2
3
4
5
queryHaploreg(query = NULL, file = NULL, study = NULL,
  ldThresh = 0.8, ldPop = "EUR", epi = "vanilla", cons = "siphy",
  genetypes = "gencode", url = Haploreg.settings[["base.url"]],
  timeout = 100, encoding = "UTF-8", querySNP = FALSE,
  fields = NULL, verbose = FALSE)

Arguments

query

Query (a vector of rsIDs).

file

A text file (one refSNP ID per line).

study

A particular study. See function getHaploRegStudyList(...). Default: NULL.

ldThresh

LD threshold, r2 (select NA to only show query variants). Default: 0.8.

ldPop

1000G Phase 1 population for LD calculation. Can be: "AFR", "AMR", "ASN". Default: "EUR".

epi

Source for epigenomes. Possible values: vanilla for ChromHMM (Core 15-state model); imputed for ChromHMM (25-state model using 12 imputed marks); methyl for H3K4me1/H3K4me3 peaks; acetyl for H3K27ac/H3K9ac peaks. Default: vanilla.

cons

Mammalian conservation algorithm. Possible values: gerp for GERP, siphy for SiPhy-omega, both for both. Default: siphy.

genetypes

Show position relative to. Possible values: gencode for Gencode genes; refseq for RefSeq genes; both for both. Default: gencode.

url

HaploReg url address. Default: <https://pubs.broadinstitute.org/mammals/haploreg/haploreg.php> Prefiously was: <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>

timeout

A timeout parameter for curl. Default: 100

encoding

sets the encoding for correct retrieval web-page content. Default: UTF-8

querySNP

A flag indicating to return query SNPs only. Default: FALSE

fields

A set of fields to extract. Refer to the package vignette for available fields. Default: All.

verbose

Verbosing output. Default: FALSE.

Value

A data frame (table) with results similar to HaploReg uses.

Examples

1
2
3
library(haploR)
data <- queryHaploreg(c("rs10048158","rs4791078"))
head(data)

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