KinInbcoefX Output File
May 25, 2009

KinInbcoefX produces two output files, here called "outputfile" and "errorfile".

   1. outputfile - a file giving the desired X-chromosome inbreeding and kinship coefficients
   2. errorfile - a file giving information on any errors in pedigreefile, namely mismatches between a parent's mother/father status and female/male sex 

1) outputfile

For each individual i listed in the listfile, outputfile gives i's X-chromosome inbreeding coefficient and the X-chromosome kinship coefficients between i
and any other members of i's family who are also listed in listfile.

outputfile contains a rectangular array of numbers, with 4 columns, and with each row corresponding to a pair of individuals (including a row for each
individual with him or herself).

The four columns are, in the following order: Family ID, Individual 1 ID, Individual 2 ID, and, lastly, either the X-chromosome inbreeding coefficient if
ID1 = ID2 or the X-chromosome kinship coefficient between individuals 1 and 2 if ID1 and ID2 are different.

Example:

       1   1   1   0.000000
       1   1   2   0.500000
       1   1   3   0.250000
       1   2   2   1.000000
       1   2   3   0.250000
       1   3   3   0.000000
       2   1   1   1.000000
       2   1   2   0.000000
       2   1   8   0.500000
       2   1   9   0.500000
       2   2   2   1.000000
       2   2   8   0.250000
       2   2   9   0.250000
       2   8   8   0.000000
       2   8   9   0.375000
       2   9   9   0.000000

      (1) (2) (3) (4)


      (1) Family ID 

      (2) Individual 1 ID 

      (3) Individual 2 ID
      
      (4) The X-chromosome inbreeding coefficient if ID1=ID2, the X-chromosome kinship coefficient otherwise

2) errorfile

If pedigreefile lists an individual's father as female or mother as male, this error will be printed to the screen as: "Error: Individual i in family f has
female father d" or "Error: Individual i in family f has male mother m", where i is the individual's ID, f is the individual's family's ID, d is the
individual's father's ID, and m is the individual's mother's ID.

errorfile contains a rectangular array of numbers, with 5 columns, and with each row describing an error of this type.

The five columns are, in the following order: family ID, individual ID, ID of the individual's parent whose sex conflicts with mother/father status, the
parent's status (1 for father, 2 for mother), and the parent's sex (1 for male, 2 for female).

Example:

Consider the example errors in pedigreefile described in Input.htm, which can be reached from the main KinInbcoefX page. In family 1, individual 2 has
individual 1 listed as a father, but individual 1 is listed as female. In family 1, individual 2 has individual 4 listed as a mother, but individual 4 is
listed as male. In family 2, individual 9 has individual 1 listed as a mother, but individual 1 is listed as male. errorfile would look like:

       1   2   1   1   2   
       1   2   4   2   1  
       2   9   1   2   1   

      (1) (2) (3) (4) (5)


      (1) Family ID 
      (2) Individual ID 
      (3) Parent ID
      (4) Parent's Status (1 for father, 2 for mother)
      (5) Parent's Sex (1 for male, 2 for female)

The program terminates after detecting all such errors.