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LD Decay

Source: vignettes/gg_LD_Decay.Rmd
gg_LD_Decay.Rmd

The function gg_LD_Decay() creates Linkage Disequilibrium (LD) Decay plots from GAPIT GWAS results.

Specifying a myG object, an outputFolder, and a markerNum is all that is needed to calculate and plot LD decay.

Note: this is a computation heavy function and the larger you set markerNum the longer the computation will take. Start by setting to a lower number such as 200 which is the default.

# Load genotype file (note: header = T)
myG <- read.csv("gwaspr_myG_hmp.csv", header = T)

markerNum = 200 

# 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 = 200 )
# 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 = 200 )
# Save
ggsave("figures/gg_LD_Decay_01.png", mp, width = 12, height = 10 )

markerNum = 2000 

# 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_02.png", mp, width = 12, height = 10 )

xx <- table_LD_Decay(
  xG = myG, 
  outputFolder = "LD_Decay/")
write.csv(xx, "LD_Summary_Table.csv", row.names = F)
##   Chr   X200  X2000
## 1   1  79592 104896
## 2   2 130852 113954
## 3   3 273983 128719
## 4   4 349679 157730
## 5   5  63173  74786
## 6   6 215886 152284
## 7   7  62221  56477
xx <- xx %>% gather(Num, Value, 2:ncol(.))
# Plot
mp <- ggplot(xx, aes(x = Chr, y = Value, fill = Num)) +
  geom_col(position = "dodge", alpha = 0.8) +
  theme_gwaspr_col(legend.position = "bottom") +
  labs(title = "LD decay", y = "Pos")
ggsave("figures/gg_LD_Decay_03.png", mp, width = 12, height = 10 )