ensemblQueryLDwithSNPregionDataframe: 'ensemblQueryLDwithSNPregionDataframe' applies...

In ensemblQueryR: Simple, Fast and Efficient Querying of the 'Ensembl' API

'ensemblQueryLDwithSNPregionDataframe' applies 'ensemblQueryLDwithSNPregion' to a data.frame of genomic coordinates and returns all variant pairs present in each specified genomic region and their associated LD metrics.

Description

'ensemblQueryLDwithSNPregionDataframe' applies 'ensemblQueryLDwithSNPregion' to a data.frame of genomic coordinates and returns all variant pairs present in each specified genomic region and their associated LD metrics.

Usage

ensemblQueryLDwithSNPregionDataframe(
  in.table,
  pop = "1000GENOMES:phase_3:EUR",
  cores = 1
)

Arguments

in.table	Dataframe containing genomic coordinates. Columns must include 'chr' (the chromosome), 'start' (the starting genomic coordinate) and 'end' (the ending genomic coordinate).
pop	String. Population for which to compute LD. Use 'ensemblQueryGetPops()' to retrieve a list of all populations with LD data. Default is 1000GENOMES:phase_3:EUR.
cores	Integer. A value between 1 and 10 is accepted, as this prevents the server returning overload-related errors.

Value

A dataframe.

Examples

## Not run: 
library(magrittr)

data.frame(
  chr=rep(c("6"), 5),
  start=rep(c("25837556"), 5),
  end=rep(c("25943455"), 5)
) %>%
  ensemblQueryLDwithSNPregionDataframe(
    in.table=.,
    pop="1000GENOMES:phase_3:EUR",
    cores = 1
  )

## End(Not run)

ensemblQueryR documentation built on May 31, 2023, 6:38 p.m.