seeker_snp_ld: seeker Single Nucleotide Polymorphism Linkage-Desequilibrium

In Erickcufe/seekerBio: Seek gen information in databases

seeker Single Nucleotide Polymorphism Linkage-Desequilibrium

Description

A function that returns LD values between the SNP and all other SNP in a window centered around the given SNP.

Usage

seeker_snp_ld(
  ID,
  population = "1000GENOMES:phase_3:MXL",
  window_size = 500,
  d_prime = 0
)

## S3 method for class 'character'
seeker_snp_ld(
  ID,
  population = "1000GENOMES:phase_3:MXL",
  window_size = 500,
  d_prime = 0
)

## S3 method for class 'factor'
seeker_snp_ld(
  ID,
  population = "1000GENOMES:phase_3:MXL",
  window_size = 500,
  d_prime = 0
)

## S3 method for class 'data.frame'
seeker_snp_ld(
  ID,
  population = "1000GENOMES:phase_3:MXL",
  window_size = 500,
  d_prime = 0
)

Arguments

ID	A Single Nucleotide Polymorphism ID ("rs") in character or data.frame
population	Population for which to compute LD. Default "1000GENOMES:phase_3:MXL"
window_size	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. Default 500
d_prime	Measure of LD. If D' is provided only return pairs of variants whose D' value is equal to or greater than the value provided. Default 0

Value

A data.frame with the LD information of SNP in a specific population

NULL

NULL

NULL

Author(s)

Erick Cuevas-Fernández

Heriberto Manuel Rivera

Source

https://rest.ensembl.org

Examples

seeker_snp_ld("rs56116432")

df <- data.frame(c("rs56116432","rs10878307", "rs7133914", "rs11564148", "rs3761863", "rs10878245"))
seeker_snp_ld(df)

Erickcufe/seekerBio documentation built on May 1, 2024, 1:13 a.m.