## crop 545 lab 5
## beagle, hapmap, imputation

black = "C:/Users/yuanh/Documents/Dropbox/COURSE/CROP_545/2018/lab5"
usb = "T:/lab5"

setwd(black)

list.files()

## 1. Get data ready ----

# 1.1 loading ----
# since the data set is too large, I have already loaded it.
# you should try and load the data 

# to avoid crashing, don't "View" your full data
fulldata = read.table("./F1-Hybrids_(Seymour_et_al_2016__PNAS)_/genotype.ped", header=T)
fulldata[1:3, 1:10]

source("hapmap2df.txt")

# 1.2 subsampling ----
myHapmap = fulldata[1:100, 1000:6001]
myGen = hapmap2df(myHapmap)


# save the data
write.csv2(myHapmap, "myHapmap.csv", row.names = F)
myHapmap = read.csv2("myHapmap.csv", header = T)

# 2. Explore the data ----


assigning missing value ----
??
  
  
# 1.