Prepares pedigree information to generate an inverse relationship matrix for use when fitting animal or plant breeding models by REML (S.A. Gezan & R.W. Payne).
Options
FREPRESENTATION = string token |
Whether to match factor values by their levels or their labels (levels, labels); default leve |
|---|---|
| SEX = string token | Possible sex categories of parents (fixed, either); default fixe |
UNKNOWN = scalar or string |
Value to be treated as unknown in the pedigree factors |
| INVMETHOD = string token | How to represent the INVERSE (full, sparse); default spar |
Parameters
INDIVIDUALS = factors |
Individuals on which data have been measured |
|---|---|
MALEPARENTS = factors |
Male parents (or sires) of the progeny |
FEMALEPARENTS = factors |
Female parents (of dams) of the progeny |
NEWINDIVIDUALS = factors |
New individuals factor, with levels standardized for use in VPEDIGREE |
NEWMALEPARENTS = factors |
New males factor, with levels standardized to match those in the NEWINDIVIDUALS factor |
NEWFEMALEPARENTS = factors |
New females factor, with levels standardized to match those in the NEWINDIVIDUALS factor |
OTHERFACTORS = pointers |
Pointer containing additional factors, that may be used in the REML models, whose levels must also be standardized to match those in the NEWINDIVIDUALS factor |
NEWOTHERFACTORS = pointers |
Pointer containing new additional factors, with standardized levels |
INVERSE = pointer |
Inverse relationship matrix in sparse matrix form |
POPULATION = variates |
Full list of identifiers generated from the individuals and parents |
Description
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 to generate a sparse inverse relationship matrix that can be used by VSTRUCTURE to define a correlation model of the individual (or animal) effects for use in a REML analysis. The matrix is formed using the VPEDIGREE directive. First, however, VPEDIGREE needs to standardize the factors so that the levels and labels of the individual male and female factors match, and that the levels are in ascending order, with the parents defined in the individuals factor before their offspring. Otherwise VPEDIGREE will fail. If you are confident that your factors are already standardized, you can call VPEDIGREE direct (and use VFPEDIGREE instead if that fails).
The factors defining the individuals, the male parents (or sires) and, optionally, the female parents (or dams) in the pedigree data set.are specified by the INDIVIDUALS, MALEPARENTS and FEMALEPARENTS parameters respectively. The OTHERFACTORS parameter can specify a pointer containing additional factors, involving the individuals in the pedigree, that may also be needed in the REML models. You can use the NEWINDIVIDUALS, NEWMALEPARENTS, NEWFEMALEPARENTS and the NEWOTHERFACTORS parameter parameters to save the new standardized factors. Otherwise, the original factors are redefined.
The FREPRESENTATION option indicates whether the factor values are to be matched by their levels (the default) or their labels. If the INDIVIDUALS, MALEPARENTS and 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.
The POPULATION option can save the levels of the standardized factors when FREPRESENTATION=levels, or their labels when FREPRESENTATION=labels.
By default, it is assumed that an individual can act as either a male or female parent but not both. Option SEX=either can be used to specify that individuals can act as both male and female parents. This may be useful, for example, in plant breeding analyses.
Missing values in any of the factors will be treated as coding for unknown individuals. Option UNKNOWN allows you to specify an additional code to represent unknown individuals. This should be a scalar (e.g. 0 or -1) when FREPRESENTATION=levels, or a single-valued text (e.g. '*' or '0') when FREPRESENTATION=labels.
The inverse relationship matrix can be saved by the INVERSE parameter. By default, this is held in a special sparse matrix form (that is, only non-zero values are stored), using a pointer. This is usable in the VSTRUCTURE directive but not elsewhere in Genstat. The second element of the pointer is a variate storing the non-zero values of the inverse matrix in lower-triangular order. The first element of the pointer is an integer index vector. Alternatively, you can set option INVMETHOD=full to store the full matrix as a symmetric matrix (which can also be used by VSTRUCTURE). However, this is not recommended for large pedigrees.
Options: FREPRESENTATION, SEX, UNKNOWN, INVMETHOD.
Parameters: INDIVIDUALS, MALEPARENTS, FEMALEPARENTS, NEWINDIVIDUALS, NEWMALEPARENTS, NEWFEMALEPARENTS, OTHERFACTORS, NEWOTHERFACTORS, INVERSE, POPULATION.
Action with RESTRICT
VFPEDIGREE ignores any restrictions on the factors.
See also
Directives: REML, VCOMPONENTS, VPEDIGREE, VSTRUCTURE, VRESIDUAL, VSTATUS.
Commands for: REML analysis of linear mixed models.
Example
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