Data processing

library(data.table)
library(plyr)
library(dplyr)
library(reshape2)
library(tidyr)
library(magrittr)

# csv_file can be found below
temp = fread(csv_file,header=T) %>% na.omit()
# method 1
temp %>% gather(rs) %>%
  dcast.data.table(rs ~ value, length) %>%
  setnames(as.character(0:2), paste0("n", 0:2)) %>%
  mutate(p = (2*n0+n1)/(2*(n0+n1+n2))) %>%
  mutate(maf = pmin(p, 1-p))

# method 2
colwise(function(x){tmp = table(x);n0 = tmp["0"]
  n1 = tmp["1"];n2 = tmp["2"];n = n0 + n1 + n2
  p=((2*n0)+n1)/(2*n);maf=pmin(p,1-p)
})(temp)

csv_file =
"rs1,rs2,rs3,rs4,rs5,rs6,rs7,rs8,rs9,rs10,rs11,rs12,rs13,rs14,rs15,rs16,rs17,rs18,rs19
0,1,1,1,1,0,1,1,0,0,0,0,0,0,0,0,0,0,0
0,2,0,0,0,1,2,0,1,0,0,2,1,1,0,1,0,0,0
0,0,0,0,0,2,0,1,0,1,1,0,0,0,0,0,0,0,0
0,2,0,1,0,2,0,1,1,1,1,0,1,1,1,1,1,0,0
1,0,1,1,1,2,1,1,0,0,0,0,2,1,1,1,0,0,0
0,2,2,2,2,1,0,0,0,0,0,0,1,0,2,0,0,0,0
0,0,0,0,0,1,0,0,0,2,2,1,1,2,0,2,0,0,0
0,0,2,1,1,1,1,1,0,1,2,1,1,2,0,2,0,0,0
1,0,1,1,1,1,0,1,0,1,2,0,0,1,0,1,NA,0,0
0,1,1,2,2,0,0,0,0,1,1,2,1,1,1,1,0,0,0
0,0,0,1,0,1,0,1,0,1,2,0,1,2,1,2,0,0,0
0,0,0,0,0,0,1,1,1,0,1,2,0,2,0,2,0,0,0
0,1,0,1,0,1,0,0,0,1,1,0,1,NA,1,0,0,0,0
1,1,0,0,0,0,1,0,0,0,0,0,1,2,0,2,0,0,0
0,2,2,2,1,1,0,1,1,1,2,0,0,1,0,1,0,0,0
0,1,1,1,1,0,0,1,2,0,1,0,1,1,0,1,1,1,1
0,1,2,2,2,0,1,1,0,0,1,1,1,0,0,0,0,0,0
0,2,1,1,1,2,2,0,0,1,1,0,1,0,2,0,0,0,0
0,2,2,2,NA,1,0,0,0,1,1,0,1,0,2,0,0,0,0
0,0,1,1,1,1,1,1,0,1,1,0,2,1,0,1,0,0,0
0,0,2,1,1,1,1,1,0,0,0,1,2,0,2,0,0,0,0
0,0,0,0,0,0,1,0,0,0,0,2,1,0,2,0,0,0,0
0,1,1,2,1,0,1,0,0,0,0,0,0,0,2,0,0,0,0
0,1,1,1,1,1,1,0,0,1,1,0,1,0,1,0,0,0,0
0,2,1,1,1,0,2,1,0,1,1,0,0,1,1,1,0,0,0
0,2,1,1,1,0,0,1,0,0,0,0,2,1,1,1,1,1,1
0,0,1,1,1,0,0,0,1,1,1,0,1,2,0,2,0,0,0
0,0,1,0,0,1,1,0,1,2,2,0,1,2,0,2,0,0,0
0,1,0,0,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0
0,1,1,1,0,0,1,0,0,0,0,1,1,1,0,1,0,0,0
1,0,2,2,2,0,0,1,0,0,0,0,2,1,1,1,0,0,0
1,1,2,2,1,2,1,0,0,1,1,0,1,1,0,0,0,0,0
0,1,1,1,1,0,1,1,0,0,0,1,2,1,1,1,1,1,1
0,1,1,1,1,1,2,0,0,0,1,0,2,0,2,0,1,1,1
0,2,1,1,1,1,0,0,0,1,1,1,2,0,2,0,0,0,0
1,1,0,0,0,0,1,0,1,0,1,0,1,1,0,1,0,0,0
0,0,1,1,1,1,1,0,0,0,1,2,0,2,0,2,0,0,0
0,1,2,1,1,0,0,1,1,0,0,1,1,0,2,0,1,1,1
0,0,1,1,1,1,1,1,1,0,0,1,0,1,1,1,0,0,0
1,0,1,1,1,2,1,1,0,0,1,1,1,1,1,1,0,0,0
0,2,1,1,1,1,1,0,0,1,1,0,0,0,1,0,0,0,0
0,1,0,0,0,1,0,2,0,0,0,0,1,1,1,1,0,0,0
0,1,0,0,0,2,2,0,0,1,1,1,1,1,1,1,0,0,0
1,1,1,1,1,0,0,0,0,0,0,0,1,0,1,0,0,0,0
0,0,0,0,0,0,2,1,0,0,1,0,0,1,0,1,0,0,0
0,0,2,2,1,1,0,0,0,0,0,2,1,1,1,1,0,0,0
0,2,1,1,1,0,1,1,0,2,2,0,2,1,1,1,0,0,0
1,1,1,1,1,1,0,1,2,0,0,0,2,0,1,0,0,0,0
1,2,1,1,1,1,0,2,0,0,0,0,2,0,1,0,0,0,0
0,2,2,2,2,0,2,1,0,0,0,0,1,0,1,0,0,0,0
1,1,1,1,1,0,0,2,1,2,2,0,1,1,0,1,0,0,0
1,2,1,1,1,2,2,1,0,0,0,0,1,1,1,1,0,0,0
0,1,1,2,1,1,1,1,1,1,1,0,0,1,0,1,0,0,0
0,1,0,0,0,1,1,2,0,1,1,1,1,1,1,1,0,0,0
0,0,2,2,2,1,0,0,0,2,2,0,0,0,0,0,0,0,0
1,0,2,2,2,1,1,1,1,0,0,0,2,1,1,0,0,0,0
0,0,2,2,2,1,0,1,1,0,1,1,1,1,1,1,0,0,0
0,0,1,0,0,0,1,1,0,1,1,1,0,2,0,2,0,0,0
2,0,0,0,0,0,0,2,0,0,0,1,1,0,1,0,1,1,1
0,1,1,2,1,1,2,1,0,0,0,0,0,2,0,2,0,0,0
0,2,1,1,1,2,1,0,0,0,0,2,1,2,0,2,0,0,0
0,1,0,0,0,0,1,0,0,1,1,0,1,0,1,0,0,0,0
0,2,1,2,1,0,1,2,0,1,1,1,0,0,0,0,0,0,0
0,0,1,1,0,1,0,1,0,2,2,2,1,1,1,1,0,0,0
0,0,0,0,0,0,0,1,0,1,1,0,1,2,0,2,0,0,0
0,1,0,1,0,1,0,1,0,1,1,0,1,2,0,2,1,1,1
0,0,1,1,1,0,0,1,0,0,1,1,1,0,0,0,0,0,0
0,1,1,1,1,1,1,1,0,0,1,0,2,1,1,1,0,0,0
0,0,1,1,1,1,0,1,0,0,0,0,1,0,0,0,0,0,0
0,2,1,1,1,1,2,2,0,0,0,0,1,0,0,0,0,0,0
0,0,0,0,0,2,1,1,0,0,0,1,1,1,1,1,0,0,0
0,1,1,1,1,0,0,2,0,0,0,1,1,1,0,1,0,0,0
0,0,1,1,1,0,2,0,1,1,1,1,1,1,1,1,0,0,0
0,0,2,2,2,1,0,0,1,0,0,0,0,2,0,2,1,1,1
0,1,2,2,2,1,1,1,0,0,0,1,0,2,0,2,0,NA,0
1,2,1,0,0,1,0,2,0,0,0,0,1,0,1,0,0,0,0
0,0,2,1,0,0,1,0,0,0,0,2,1,1,0,1,0,0,0
1,0,2,1,1,1,2,0,0,0,1,0,0,1,0,1,0,0,0
0,2,1,1,0,0,0,1,0,0,1,0,1,0,1,0,0,0,0
1,1,0,0,0,1,1,2,0,0,0,0,2,0,2,0,0,0,0
0,0,0,0,0,1,0,1,1,0,0,1,0,1,0,1,0,0,0
0,1,NA,2,2,0,1,0,1,0,0,1,2,0,1,0,0,0,0
0,0,0,0,0,0,1,0,0,0,0,1,0,1,0,1,0,0,0
0,0,0,0,0,0,2,1,0,1,1,1,1,1,0,1,0,0,0
0,2,0,0,0,1,0,0,0,0,1,0,2,0,2,0,0,0,0
0,0,1,1,1,1,1,1,0,0,1,0,1,1,0,1,0,0,0
0,0,2,2,1,2,0,1,0,2,2,0,0,1,1,1,0,0,0
0,0,1,1,1,1,0,0,0,1,1,0,1,1,1,0,0,0,0
0,1,0,0,0,1,0,0,0,1,1,0,0,0,1,0,0,0,0
0,1,0,1,1,2,1,1,0,1,1,1,0,1,0,1,0,0,0
0,1,1,2,1,2,0,1,0,0,1,0,1,1,1,1,0,0,0
0,1,1,0,0,0,0,1,0,0,0,0,2,1,1,0,0,0,0
1,1,0,1,0,1,1,0,0,0,0,0,1,2,0,1,0,0,0
0,1,1,1,1,0,1,2,1,0,0,1,1,0,0,NA,0,0,0
0,1,1,0,0,1,1,1,0,1,1,0,2,0,2,0,2,2,2
0,2,0,0,0,0,0,0,0,0,0,0,2,1,1,1,0,0,0
0,1,0,0,0,0,1,2,0,1,1,1,2,1,0,1,0,0,1
0,2,0,0,0,1,0,0,0,0,1,1,0,1,1,1,0,0,1
1,1,0,0,0,1,1,0,0,0,1,0,0,1,0,1,0,0,0
0,0,0,0,0,1,1,0,1,0,0,1,0,2,0,2,0,0,0
0,0,1,1,1,1,1,1,0,1,1,0,1,1,0,1,0,0,0
0,2,1,1,1,1,1,0,0,0,0,0,1,0,0,0,0,0,0
0,0,1,1,0,0,1,1,0,0,1,0,1,2,0,2,0,0,0
1,1,2,2,1,0,1,0,0,1,1,0,1,1,0,1,0,0,0
1,1,0,0,0,1,0,0,0,0,2,1,1,1,0,1,1,1,1
0,2,2,2,2,0,2,1,0,1,1,0,1,0,0,0,0,0,0
0,1,0,0,0,1,1,0,0,0,1,0,0,0,0,0,0,0,0
0,1,0,0,0,1,0,1,0,1,1,1,2,2,0,2,0,0,0
0,0,1,2,1,0,0,0,1,1,1,1,0,1,1,1,0,0,0
0,0,0,0,0,1,1,0,1,1,2,0,0,0,1,0,0,0,0
1,0,1,1,1,1,1,0,0,0,0,0,2,1,1,1,0,0,0
0,0,1,0,0,1,0,1,0,0,1,1,1,1,0,1,0,0,0
0,0,1,1,1,1,0,1,0,1,1,0,1,0,2,0,0,0,0
1,2,1,1,1,1,0,0,0,1,1,1,1,2,0,2,0,0,0
0,0,2,2,2,1,1,0,0,0,1,2,0,1,0,1,0,0,0
0,0,0,0,0,0,1,1,0,0,1,0,1,1,1,1,0,0,0
0,2,2,1,1,0,0,1,0,0,1,0,1,2,0,1,0,0,0
0,2,1,1,0,2,1,0,1,0,1,0,2,1,0,0,0,0,0
0,0,1,1,1,1,1,1,1,0,0,0,2,0,2,0,0,0,0
0,1,0,0,0,2,0,1,0,0,0,1,0,2,0,2,0,0,1
0,0,2,2,1,2,0,2,1,1,1,0,1,0,0,0,0,0,0
0,2,0,0,0,0,0,0,0,1,1,0,2,0,1,0,0,0,0
0,0,1,1,0,1,1,1,0,0,0,0,1,0,0,0,0,0,0
1,1,2,2,2,1,0,1,0,0,0,0,1,0,1,1,0,0,0
0,0,0,0,0,1,1,1,0,0,0,1,1,1,1,1,0,0,0
1,0,2,1,0,0,0,0,0,1,1,0,1,0,0,0,0,0,0
1,0,1,1,1,0,0,0,0,0,0,1,1,1,1,1,0,0,0
0,1,1,2,1,2,0,1,0,0,0,1,2,1,1,1,1,1,1
0,1,0,1,0,0,0,1,0,0,1,0,2,2,0,1,0,0,0
0,0,2,2,1,2,2,0,1,1,1,0,2,1,1,1,0,0,0
1,1,0,0,0,0,0,1,0,0,1,0,0,1,0,1,0,0,0
1,0,2,2,1,0,1,1,0,0,0,0,1,1,0,1,0,0,0
0,2,2,2,2,2,2,1,0,0,0,1,0,1,0,1,0,0,0
0,0,0,0,0,0,0,0,0,0,1,0,1,0,2,0,0,0,0
0,0,1,1,0,2,2,1,0,0,0,1,1,0,1,0,0,0,0
0,0,0,0,0,1,0,1,0,0,0,0,1,2,0,2,0,0,0
0,0,1,1,1,0,2,0,0,1,2,0,0,1,0,1,0,0,0
1,0,2,2,2,1,1,1,1,0,0,0,2,1,1,0,0,0,0
0,1,2,2,2,1,0,0,0,1,1,0,1,0,1,0,0,0,0
1,1,1,2,1,0,1,1,0,1,2,1,0,0,1,0,0,0,0
0,0,2,2,2,0,0,1,1,0,0,0,2,1,1,1,0,0,0
1,1,1,1,1,0,0,1,0,0,0,0,1,1,1,1,0,0,0
0,1,1,1,1,0,0,1,0,1,2,0,0,0,0,0,0,0,0
2,0,0,0,0,0,0,2,0,0,0,1,1,0,1,0,1,1,1
0,0,1,1,0,1,0,2,0,0,0,0,1,0,1,0,1,1,1
0,1,1,1,1,1,0,2,0,0,1,0,0,1,0,1,0,0,0
1,0,1,1,1,2,1,1,0,0,0,0,2,1,1,1,0,0,0
0,1,1,1,1,0,0,0,0,2,2,0,1,0,0,0,0,0,0
0,1,2,2,2,0,0,1,0,0,0,0,2,0,2,0,0,0,0"