seeker_snp_ld_plot: seeker_snp_ld_plot

In Erickcufe/seekerBio: Seek gen information in databases

seeker_snp_ld_plot

Description

A function that plot the Linkage-Dsequilibrium information for a given Single Nucleotide Polymorphism

Usage

seeker_snp_ld_plot(
  SNP,
  population_study = "1000GENOMES:phase_3:MXL",
  window_size = 500,
  d_prime = 0,
  color_select = "cyan",
  plot_all = TRUE,
  r_2 = 0.25
)

Arguments

SNP	A Single Nucleotide Polymorphism ID ("rs") in character.
population_study	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
color_select	Select a color for the plot; Default= "cyan"
plot_all	If TRUE, the function plot all the labels of SNPs with a r2 > 0.6. If it is FALSE, the function only plot the label of the SNP

Value

A plot, in x axis the position in the chromosome, in y axis the r2 of linkage desequilibrium

Author(s)

Erick Cuevas Fernández

Heriberto Manuel Rivera

Examples

seeker_snp_ld_plot("rs7412", "1000GENOMES:phase_3:MXL", color_select = "green")

seeker_snp_ld_plot("rs7412", "1000GENOMES:phase_3:SAS", color_select = "pink")

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