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ensemblQueryR

DOI

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: for one query SNP

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

To get a list of possible human Ensembl populations to use in the pop argument, run the ensemblQueryGetPops() function.

ensemblQueryR::ensemblQueryGetPops()

Example: for <1000 query SNPs

rsid.list <- c("rs7153434","rs1963154","rs12672022","rs3852802","rs12324408","rs56346870")

# run query on rsid.list
ensemblQueryR::ensemblQueryLDwithSNPlist(rsid.list, 
                          r2=0.8, 
                          d.prime=0.8, 
                          window.size=500, 
                          pop="1000GENOMES:phase_3:EUR")

Example for >1000 query SNPs

There is a separate function for large queries (>1000 SNPs) because of Ensembl's API query size limit. This function takes a data.frame as an input, and gets all SNPs in LD with a column containing query SNPs called rsid.

# example input data
in.table <- data.frame(rsid=rep(c("rs7153434","rs1963154","rs12672022","rs3852802","rs12324408","rs56346870"), 500))

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

Disclaimer

Please note that this code is still under development and may contain bugs or errors. It is not recommended for use in production environments. Use at your own risk. I am working on improving the code, addressing any issues, and expanding the package's capabilities so please check back for updates.