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4.1 Introduction to kin
4.2 Sample kin
parameter file4.3 Running kin
example and sample output4.4 kin
statements
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kin
kin
computes kinship coefficients for pairs of pedigree members. It also
computes single-locus and two-locus inbreeding coefficients for members of the
pedigree. Briefly, the kinship coefficient between individuals i and j
is the probability that a randomly-drawn allele from i is identical by
descent (ibd) to randomly-drawn allele from individual j at the same
locus. A single-locus inbreeding coefficient is the probability that an
individual carries two copies of a gene that are ibd, at a given autosomal
locus. In other words, an individual's single-locus inbreeding coefficient is
equal to the kinship coefficient of his parents, as an individual's gametes can
be thought of as random draws from his parents' chromosomes. A two-locus
inbreeding coefficient is the probability that an individual carries two ibd
copies of a gene at each of two linked loci. kin
presents two-locus
inbreeding coefficients as a function of the recombination fraction between the
two loci.
Note: The kin
program does check for duplicate requests
within a pedigree component of any inbreeding or kinship coefficients;
each will be computed once only, even if the individuals are specified
in reverse order.
However, it does
check (and quits with an error) if a request is made for kinship of an
individual with him/her self. This bug will be fixed in a future
MORGAN release.
See Concept Index for:
kin
introduction,
kinship coefficient,
inbreeding coefficient,
ibd,
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kin
parameter file
Files for kin
may be found in the `IBD' subdirectory of
`MORGAN_Examples'.
Below is a sample kin
parameter file, `jv_rep_kin.par'.
set printlevel 5 input pedigree file 'jv_rep.ped' compute component 1 kinship coeff 531 431 431 432 compute component 1 inbreeding coeff 332 531 compute component 2 kinship coeff 341 442 compute component 2 inbreeding coeff 441 541 compute component 1 two-locus inbreed coeff 531 compute component 2 two-locus inbreed coeff 441 set recomb freqs .01 .05 .04 .10 .18 .30 .50 .0 |
The statements on lines 3 -- 8 request computation of kinship coefficients for
the pairs `531 431' and `431 432', and then inbreeding coefficients
for individuals `332' and `531', from component 1. It then requests
kinship coefficients for the pair `341 442' and inbreeding coefficients for
individuals `441' and `541' from component 2. Finally, it requests
the two-locus inbreeding coefficient for `531' from component 1 and
`441' from component 2. The two-locus inbreeding coefficient will be
computed for two loci at distances specified in the `set recomb freqs'
statement. (Note these need not be ordered, but the program will order them in
the output.) If there is more than one component (connected pedigree) in the
file, the component number must be specified. MORGAN assigns
component numbers to the connected pedigrees within the pedigree file. If your
data set contains more than one component, you may first run pedcheck
to
determine which individuals are assigned which component numbers.
See Concept Index for:
kin
sample parameter file.
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kin
example and sample output Under the subdirectory `IBD/', run the example above using the command below. To send the output to a file instead of the screen, include `> filename' (without quotes) after the parameter file name on the command line:
./kin jv_rep_kin.par or ./kin jv_rep_kin.par > out-file-name |
Below is the relevant part of the kin
output.
Component 1: Kinship coefficients: 531 431 .32031 431 432 .10938 Inbreeding coefficients: 332 .00000 531 .10938 2-locus inbreeding coefficients: (g4link is probability of IBD at both of 2 linked loci) proband recomb g4link freq prob 531 .000 .10938 .010 .10234 .040 .08386 .050 .07849 .100 .05660 .180 .03455 .300 .01910 .500 .01196 Component 2: Kinship coefficients: 341 442 .15625 Inbreeding coefficients: 441 .06250 541 .10938 2-locus inbreeding coefficients: (g4link is probability of IBD at both of 2 linked loci) proband recomb g4link freq prob 441 .000 .06250 .010 .05885 .040 .04905 .050 .04614 .100 .03388 .180 .02060 .300 .01008 .500 .00391 |
Note that when the recombination frequency is 0.0, the two-locus inbreeding coefficient is the same as the one-locus inbreeding coefficient, as there is no recombination between the loci, thus they act as a single locus. When the recombination frequency is 0.5, the two loci are independent and the two-locus inbreeding coefficient is the square of the one-locus inbreeding coefficient.
See Concept Index for:
running kin
example,
kin
sample output.
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kin
statements
At least one of the following `compute ...' statements are required to run
program kin
. If there is more than one component (connected pedigree) in
the file, the component number must be specified. MORGAN assigns
component numbers to the connected pedigrees within the pedigree file. If your
data set contains more than one component, you may first run pedcheck
to
determine which individuals are assigned which component numbers.
pedcheck
will sort by component number in the output pedigree file,
although it will not list component numbers in the file. The screen output
generated when running pedcheck
will give component numbers and the
number of individuals in each component. Check the error and warning messages
when running kin
to verify that component numbers were correctly
specified. The program will quit if an individual's component number is
incorrectly specified in the parameter file or if there is more than one
component in the data set and no component is specified.
compute [component M] kinship coefficient N1 N2...
This statement names one or more pairs of pedigree members for which the kinship coefficient is to be computed.
compute [component M] inbreeding coefficient N1...
This statement names one or more pedigree members for whom the inbreeding coefficient is to be computed.
compute [component M] two-locus inbreeding coefficient N1...
This statement requests the computation of two-locus inbreeding coefficients, i.e. the probability of ibd at both loci, for the named individual. For the recombination frequencies at which the coefficients are computed, see the following statement.
set recombination frequencies X1 X2...
Two-locus inbreeding coefficients are computed for each of the list of recombination frequencies, in the range of 0.0 to 0.5. If frequencies are not given, the default values are: 0.0, 0.01, 0.04, 0.05, 0.10, 0.18, 0.30, and 0.50.
See Concept Index for:
kin
statements,
component,
pedigree component,
kinship coefficient,
inbreeding coefficient,
recombination.
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