QKINSHIPMATRIX procedure

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
METHOD = string token	Method to use for the calculation (correlation, dice); default dice

Parameters

MKSCORES = pointers	Pointer with the marker scores; must be set
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'