ensemblQueryLDwithSNPwindow: Function to query Ensembl LD data with a single rsID
Description
Function to query Ensembl LD data with a single rsID
Usage
ensemblQueryLDwithSNPwindow(
rsid,
pop = "1000GENOMES:phase_3:EUR",
r2 = NA,
d.prime = NA,
window.size = NA
)
Value
A dataframe.
Arguments
rsid
String. Variant ID.
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.
r2
Float. Measure of LD. If r-squared is provided only return pairs of variants whose r-squared value is equal to or greater than the value provided.
d.prime
Float. Measure of LD. If D' is provided only return pairs of variants whose D' value is equal to or greater than the value provided.
window.size
Integer. Window size in kb. The maximum allowed value for the window size is 500 kb. LD is computed for the given variant and all variants that are located within the specified window.