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LD Decay

Source: vignettes/gg_LD_Decay.Rmd
gg_LD_Decay.Rmd

The function gg_Volcano() creates volcano plots from GAPIT GWAS results.

Specifying a folder and trait is all that is needed to create manhattan plots.

# Load genotype file (note: header = T)
myG <- read.csv("gwaspr_myG_hmp.csv", header = T)
# Calulate LD decay
calc_LD_Decay(
  # Load genotype data
  xG = myG,
  # Specify a folder with GWAS results
  outputFolder = "LD_Decay/",
  # Select the number of markers per chromosome to analyse
  markerNum = 2000 )
# Plot
mp <- gg_LD_Decay(
  # Load genotype data
  xG = myG,
  # Specify a folder with GWAS results
  outputFolder = "LD_Decay/",
  # Select the number of markers per chromosome to analyse
  markerNum = 2000 )
# Save
ggsave("figures/gg_LD_Decay.png", mp, width = 12, height = 10 )