ensemblQueryR (version 0.1.0)

ensemblQueryLDwithSNPregionDataframe: `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
)

Value

A dataframe.

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.

Examples

if (FALSE) {
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
  )
}