[R] Using R to Calculate Coefficients of Relatedness and Kinship for Family Members

[JS Huang]

Hi,

  I don't quite understand the logic since some later assignment will
overwrite the previous one.  I simply assign for the current index and
ignore the index after it.  In addition, the column Dads.Renamed is not in
the data.frame you defined in the post and I used Father_ID to substitute
for it.  Here is an implementation.  Write back if this is not what you
expect.

> pedigree.data
   Subject Twin_Stat Zygosity Father_ID Mother_ID
1   100307      Twin    NotMZ     81352     51488
2   100408      Twin       MZ     81594     51730
3   101006      Twin       MZ     81149     51283
4   101107   NotTwin  NotTwin     81833     51969
5   101309   NotTwin  NotTwin     82248     52385
6   101410      Twin    NotMZ     82061     52198
7   101915   NotTwin  NotTwin     81841     51977
8   102008   NotTwin  NotTwin     81882     52018
9   102311      Twin       MZ     81543     51679
10  102816      Twin       MZ     81283     51418
> assignKinScore
function(Input)
{
  result <- rep(0,dim(Input)[1] - 1)
  for (i in 1:(dim(Input)[1] - 1))
  {
    if (as.character(Input$Twin_Stat[i]) == "Twin" &
as.character(Input$Twin_Stat[i + 1]) == "Twin")
    {
      if (as.character(Input$Zygosity[i]) == "MZ" &
as.character(Input$Zygosity[i + 1]) == "MZ")
      {
        result[i] <- 0.5
      }
      else
      {
        if (as.character(Input$Zygosity[i]) == "DZ" &
as.character(Input$Zygosity[i + 1]) == "DZ")
        {
          result[i] <- 0.25
        }        
      }
    }
    else
    {
      if (as.character(Input$Twin_Stat[i])=="NotTwin" &
as.character(Input$Twin_Stat[i + 1])=="NotTwin")
      {
        if (Input$Mother_ID[i] == Input$Mother_ID[i + 1] &
Input$Father_ID[i] == Input$Father_ID[i + 1])
        {
          result[i] <- 0.25
        }
        else
        {
          if (Input$Mother_ID[i] == Input$Mother_ID[i + 1] &
Input$Father_ID[i] != Input$Father_ID[i + 1])
          {
            result[i] <- 0.125
          }        
        }
      }
    }
  }
  return(result)
}
> assignKinScore(pedigree.data)
[1] 0.0 0.5 0.0 0.0 0.0 0.0 0.0 0.0 0.5



-----
JS Huang
--
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