||Whether to match factor values by their levels or their labels (
||Value to be treated as unknown in the pedigree factors|
||Individuals on which data have been measured|
||Male parents (or sires) of the progeny|
||Female parents (of dams) of the progeny|
||New individuals factor, with levels standardized for use in
||New males factor, with levels standardized to match those in the
||New females factor, with levels standardized to match those in the
||Pointer containing additional factors, that may be used in the
||Pointer containing new additional factors, with standardized levels|
In the analysis of animal and plant breeding experiments it may be interesting to take account of the parentage of the animals or genotypes. This pedigree information is specified by three factors, one that identifies the individuals for which data are available, and two others that indicate their male parents and their female parents (if available). This information can be used by the
VPEDIGREE directive to generate a sparse inverse relationship matrix that can then be used by
VSTRUCTURE to define a correlation model of the individual (or animal) effects for use in a
VPEDIGREE, however, can only use the levels to match the male and female factors with the individuals, those levels must be in ascending order, and the parents must be defined in the individuals factor before their offspring. So
VFPEDIGREE has been provided to allow sets of pedigree factors to be checked and pre-processed, to ensure that they can be used successfully as input for
INDIVIDUALS parameter specifies a factor to define the individuals in the pedigree data set. The
MALEPARENTS parameter specifies a factor to identify their male parents (or sires), and the
FEMALEPARENTS parameter optionally specifies a factor to identify their female parents (or dams). The new modified factors can be saved using the
NEWFEMALEPARENTS parameters. The
OTHERFACTORS parameter allows you to specify a pointer containing additional factors, involving the individuals in the pedigree, that may be needed in the
REML models. Factors to store the standardized versions of these other factors can be supplied, again in a pointer, using the
FREPRESENTATION option indicates whether the factor values are to be matched by their levels (the default) or their labels. If the
FEMALEPARENTS factors are being matched by levels, and the number corresponding to each level needs to be redefined, the factors will be given labels to help identify the original values. If
INDIVIDUALS has labels, these will be used. Otherwise the labels will be textual forms of the original levels.
Missing values in any of the factors will be treated as coding for unknown individuals. Option
UNKNOWN allows you to specify an additional to represent unknown individuals. This should be a scalar (e.g. 0 or -1) when
FREPRESENTATION=levels, or a single-valued text (e.g.
VFPEDIGREE ignores any restrictions on the factors.
Commands for: REML analysis of linear mixed models.
CAPTION 'VFPEDIGREE example'; STYLE=meta " Basic example of animal model" " Read the data: pedigree and response (in the same file)" " with levels all Individuals" FACTOR [NVALUES=5; LEVELS=!(3,4,5,6,7)] Indiv & [LEVELS=!(0,1,3,5)] Sire & [LEVELS=!(0,2,4,6)] Dam VARIATE [NVALUES=5] Size READ Indiv,Sire,Dam,Size; 3 1 0 12.8 4 1 2 14.5 5 3 4 11.2 6 1 4 12.6 7 5 6 9.9 : VFPEDIGREE [FREPRESENTATION=levels; UNKNOWN=0] Indiv; NEWIndivIDUALS=ID_Indiv;\ MALEPARENTS=Sire; NEWMALEPARENTS=ID_Sire;\ FEMALEPARENTS=Dam; NEWFEMALEPARENTS=ID_Dam;\ OTHERFACTORS=!p(Indiv); NEWOTHERFACTORS=!p(f_Indiv) VPEDIGREE [SEX=fixed] ID_Indiv; MALEPARENTS=ID_Sire; INVERSE=AINV;\ FEMALEPARENTS=ID_Dam VCOMPONENTS RANDOM=f_Indiv; CONSTRAINTS=pos VSTRUCTURE [TERMS=f_Indiv] MODEL=fixed; INVERSE=AINV REML [PRINT=model,components,means; PARAM=sigmas] Size