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ensemblQueryR

GitHub https://img.shields.io/github/last-commit/ainefairbrother/ensemblQueryR

The goal of ensemblQueryR is to seemlessly integrate querying of Ensembl databases into your R workflow. It does this by formatting and submitting user queries to the Ensembl API. In its current iteration, the package can retreive SNPs in LD with any number of query SNPs.

Installation

You can install the development version of ensemblQueryR like so:

remotes::install_github("ainefairbrother/ensemblQueryR")

Example

library(ensemblQueryR)
library(magrittr)

# for one query SNP: get all SNPs in LD with query SNP
ensemblQueryLDwithSNP(rsid="rs3851179", 
                      r2=0.8, 
                      d.prime=0.8, 
                      window.size=500, 
                      pop="1000GENOMES:phase_3:EUR")

# for fewer than 1000 query SNPs: get all SNPs in LD with a list of query SNPs
ensemblQueryLDwithSNPlist(rsid.list, 
                          r2=0.8, 
                          d.prime=0.8, 
                          window.size=500, 
                          pop="1000GENOMES:phase_3:EUR")

# for more than 1000 query SNPs: get all SNPs in LD with a data.frame column of query SNPs
# example input data
in.table <- data.frame(rsid=rep(c("rs7153434","rs1963154","rs12672022","rs3852802","rs12324408","rs56346870"), 500))

# run query on in.table
ensemblQueryLDwithLargeSNPdf(in.table=in.table,
                             r2=0.8,
                             d.prime=0.8,
                             window.size=500,
                             pop="1000GENOMES:phase_3:EUR")