gg_NYCvsKansas()

library(gwaspr)

GAPIT

checkNYCvsKansas()

The function checkNYCvsKansas() will output a table indicating the number of markers with different p values between NYC and Kansas files.

Specifying a folder of GWAS results is all that is needed for this function.

checkNYCvsKansas(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/", 
  # Delete any Kansas files with no difference between the NYC files if set to T
  deleteKansas = F )

##                   Trait FarmCPU BLINK
## 1 Cotyledon_RedvsYellow      76     1
## 2        DTF_Nepal_2017     731     0
## 3         DTF_Sask_2017     584     0
## 4       DTF_Sask_2017_b     543     0

The function gg_NYCvsKansas() creates manhattan plots from GAPIT GWAS results.

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

mp <- gg_NYCvsKansas(
  # Specify a folder with GWAS results
  folder = "GWAS_Results/",
  # Specify a trait to plot
  trait = "DTF_Nepal_2017"
)
# Save
ggsave("figures/gg_NYCvsKansas.png", mp, width = 12, height = 5)