Forms a kinship matrix from molecular markers (L.C.P. Keizer & J.T.N.M. Thissen).
Options
PRINT = string token |
What to print (summary); default summ |
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METHOD = string token |
Method to use for the calculation (correlation, dice); default dice |
Parameters
MKSCORES = pointers |
Pointer with the marker scores; must be set |
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IDMGENOTYPES = texts |
Labels for the genotypes |
KMATRIX = symmetric matrices |
Saves the kinship matrix |
OUTFILENAME = texts |
Name of the file to receive the kinship matrix |
Description
QKINSHIPMATRIX forms a kinship matrix from the marker scores specified by the MKSCORES parameter. The IDMGENOTYPES parameter can provide a text with row (and column) labels for the matrix.
The METHOD option specifies the method to use to calculate the coefficients of coancestries of the kinship matrix, with settings:
dice |
calculates the similarities by the FSIMILARITY directive with test type dice, and |
|---|---|
correlation |
uses simple correlation coefficients. |
The kinship matrix can be saved using the KMATRIX parameter, in a symmetic matrix. It can also be saved in an output file, by supplying the file name using the OUTFILENAME parameter.
By default QKINSHIPMATRIX prints summary information about the marker scores and the method used, but you can set option PRINT=* to suppress this.
Options: PRINT, METHOD.
Parameters: MKSCORES, IDMGENOTYPES, KMATRIX, OUTFILENAME.
Action with RESTRICT
Restrictions are not allowed.
See also
Procedure: QSASSOCIATION.
Commands for: Statistical genetics and QTL estimation.
Example
CAPTION 'QKINSHIPMATRIX example'; STYLE=meta
QIMPORT [POPULATION=AMP] '%GENDIR%/Examples/LD_example_geno.txt';\
MAPFILE='%GENDIR%/Examples/LD_example_map.txt';\
MKSCORES=mkscores; CHROMOSOMES=mkchr; POSITIONS=mkpos;\
MKNAMES=mknames; IDMGENOTYPES=idmgeno
QKINSHIPMATRIX mkscores; IDMGENOTYPES=idmgeno;\
KMATRIX=kmat; OUTFILENAME='LD_example_kinship.gsh'