5.4 caseparents.dat

caseparents.dat: This file contains a header line (which is not read in by the program but is useful for reminding yourself of the column order), followed by a line of data for each of the n SNPs to be analysed (IN EXACTLY THE SAME ORDER as given in emimmarkers.dat).

The first number on each line is the numeric SNP ID (as given in emimmarkers.dat). This is followed by 9 cell counts corresponding to the number of fully genotyped parents of cases whose genotype combinations fall into the appropriate genotype categories. Note that these parents of cases must not include parents of cases who have already appeared as case/parent trios in the file caseparenttrios.dat (i.e. all input data files must be independent).

For example, suppose that at the first SNP the genotype combinations of the mother and father are

group mother father count
1 22 22 0
2 22 12 0
3 22 11 1
4 12 22 0
5 12 12 0
6 12 11 0
7 11 22 0
8 11 12 2
9 11 11 16

Then the line in caseparents.dat corresponding to this SNP would look like: 

1     0 0 1 0 0 0 0 2 16

An example of caseparents.dat for 8 SNPs, of which the first has counts as given above, is shown below: 

snp cellcount 1-9
1     0 0 1 0 0 0 0 2 16
2     0 0 0 0 1 3 0 1 9
3     0 0 0 0 0 0 0 0 13
4     0 0 1 0 0 0 0 0 1
5     0 0 0 0 1 0 0 1 0
6     0 0 0 0 0 0 0 0 0
7     0 0 0 0 0 0 1 0 0
8     0 0 1 0 0 1 0 3 0

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