Checks and prepares pedigree information from several factors, for use by VPEDIGREE and 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 |
|---|---|
UNKNOWN = scalar or string |
Value to be treated as unknown in the pedigree factors |
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 |
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 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 REML analysis. 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 VPEDIGREE.
The 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 NEWINDIVIDUALS, NEWMALEPARENTS and 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 NEWOTHERFACTORS parameter.
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.
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. '*' or '0') when FREPRESENTATION=labels.
Options: FREPRESENTATION, UNKNOWN.
Parameters: INDIVIDUALS, MALEPARENTS, FEMALEPARENTS, NEWINDIVIDUALS, NEWMALEPARENTS, NEWFEMALEPARENTS, OTHERFACTORS, NEWOTHERFACTORS.
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