Sib-pair Command: hbd (homozygosity by descent)


ClassAnalysis and data manipulation command
Namehbd (homozygosity by descent)
Arguments <codominant marker> [<coef_variable>].

Print MCMC (Markov Chain Monte-Carlo) estimates of the homozygosity by descent for a marker locus. This can be saved to a quantitative trait variable if requested.

Example:

>> include alopeciaex.in
>> hbd D8S1786
-------------------------------------------------------
Estimated homozygosity-by-descent at locus "D8S1786"
-------------------------------------------------------
Pedigree   ID          HBD    F       Gtp
AU         101        0.0000 0.0000   x/x
AU         102        0.0000 0.0000   x/x
AU         202        0.0000 0.0000   x/x
AU         204        0.0000 0.0000   x/x
...
AU         603        0.0000 0.1094   1/5
AU         604        0.3650 0.1094   5/5
AU         605        0.1250 0.1094   x/x
AU         606        0.2050 0.1094   x/x
AU         607        0.3350 0.1094   5/5
AU         608        0.0000 0.1094   1/5
AU         609        0.0000 0.0859   1/5
AU         610        0.0000 0.0859   1/5
AU         611        0.0000 0.0859   x/x
AU         612        0.0000 0.0859   x/x

>> set loc inb qua
Creating new variable "inb".

>> kin inb inb
Writing inbreeding coefficient to "inb"

Mean inbreeding coefficient =  0.038043 (based on 69 nonfounder individuals)
Number of inbred individuals= 37

>> set loc hdb qua
Creating new variable "hbd".

>> hbd D8S1786 hbd

-------------------------------------------------------
Estimated homozygosity-by-descent at locus "D8S1786"
-------------------------------------------------------
Writing HBD to "hbd"

>> reg alopecia = inb
>> reg alopecia = inb hbd
>> lrt

Term         -2*LL NPar  P-value
------ ----------- ----  -------
Model0     58.8399    2
Model1     45.3380    3
LRTS       13.5020    1  0.0002


<< (ibs)Up to index>> (cksib)