dat <- data.frame(s=c(1,1,1,1,2,2,2,2,3,3,3,3),
                 c1=c("w","x","y","z","w","x","y","z","w","x","y","z"),
                 c2=c("m","m","m","m","f","f","f","f","m","m","m","m"),
                 c3=c(1,2,3,4,5,6,7,8,9,10,11,12))

> dat
       s c1 c2 c3
    1  1  w  m  1
    2  1  x  m  2
    3  1  y  m  3
    4  1  z  m  4
    5  2  w  f  5
    6  2  x  f  6
    7  2  y  f  7
    8  2  z  f  8
    9  3  w  m  9
    10 3  x  m 10
    11 3  y  m 11
    12 3  z  m 12

s  diff  c2  c3
1  w-x   m   -1
1  w-y   m   -2
1  w-z   m   -3
1  x-y   m   -1
etc