KinInbcoefX is a C++ program that recursively calculates X-chromosome kinship and inbreeding coefficients in arbitrarily related individuals based on pedigree and sex information.
We use the following definition: the X-chromosome kinship coefficient, C_AB, for individuals A and B, is the probability that a pair of alleles chosen at random, one from A and one from B, at a non-pseudoautosomal locus on the X-chromosome, is identical by descent. For instance, by this definition, C_AB=.25 for an outbred mother-daughter pair, .5 for an outbred mother-son pair, .5 for an outbred father-daughter pair, and 0 for an outbred father-son pair. The X-chromosome inbreeding coefficient for a male is always defined to be 1, regardless of whether there is inbreeding. The X-chromosome inbreeding coefficient for a female is defined to be the X-chromosome kinship coefficient between her parents (which would be 0 for an outbred female).
The program takes the following as input:
The formats of the input and output files are provided in Input.htm and Output.htm to which you can link from the main KinInbcoefX page. The main page also links to Download.htm, where all files related to the program are available for download. These files include descriptions of input and output, a README file, sample test files, the source code, and pre-compiled code.
On the command line, following "./KinInbcoefX ", four arguments should be entered in the following order: name of the pedigreefile, a space, name of the listfile, a space, name of the outputfile, a space, and name of the errorfile.
A C++ compiler should be used to compile the program. When using the g++ compiler, type: g++ KinInbcoefX.c -o KinInbcoefX
There are two examples using correct input. The first example is more complicated than the second example. The second example is the same as that given in webpages Input.htm and Output.htm, which are accessible from the KinInbcoefX main page.
Input files "pedtestX", "listtestX", and "outtestX" correspond to the first example. Input files "pedtestX2", "listtestX2", and "outtestX2" correspond to the second example. All these example files can be found in Download.htm, to which you can link from the main page.
To run the program using the first example input files, type:
./KinInbcoefX pedtestX listtestX out error
and compare the results in the "out" file with the results in the "outtestX" file. error should be an empty file.
Similarly, to run the program using the second example input files, type:
./KinInbcoefX pedtestX2 listtestX2 out2 error2
and compare the results in the "out2" file with the results in the "outtestX2" file. error2 should be an empty file.
There is one example that demonstrates what a non-blank errorfile would look like. To run the program using second example listfile and incorrect second example pedigreefile, type:
./KinInbcoefX pedtestX2.Error listtestX2 out2.Error error2.Error
Since the program terminates when an error occurs, out2.Error should be an empty file. Descriptions of errors should be printed to the screen, and information on errors should be contained in error2.Error, which should be the same as the provided file errortestX2.Error.
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