ASReml-S reference manual - VSN International

5.3 Generating an A-inverse matrix with asreml.Ainverse() 5712 Sire_9 G3 G313 101 Sire_1 G114 102 Sire_1 G115 103 Sire_1 G116 104 Sire_1 G117 105 Sire_1 G118 106 Sire_1 G119 107 Sire_1 G120 108 Sire_1 G1It is usually appropriate to allocate a genetic group identifier where the parent is unknown.5.3 Generating an A-inverse matrix with asreml.Ainverse()asreml.Ainverse() uses the method of Meuwissen and Luo [1992] to compute the inverserelationship matrix directly from the pedigree. A complete description of the argumentsand return value of a call to asreml.Ainverse() is:asreml.Ainverse(pedigree, groups=0, selfing=NA, inBreed=NA, mgs=FALSE)Required argumentspedigreeOptional argumentsgroupsselfinginBreedmgsValuea list with the following components:A data frame with three columns that correspond to the individual,male parent and female parent, respectively. The row giving thepedigree of an individual must appear before any row where thatindividual appears as a parentincludes genetic groups in the pedigree. The first g lines of the pedigreeidentify genetic groups (with zero in both the male and femaleparent columns). All other rows must specify one of the genetic groupsas sire or dam if the actual parent is unknown.allows for partial selfing when the third field of pedigree is unknown. Itindicates that progeny from a cross where the male parent is unknownis assumed to be from selfing with probability s and from outcrossingwith probability (1 − s). This is appropriate in some forestry treebreeding studies where seed collected from a tree may have been pollinatedby the mother tree or pollinated by some other tree (Dutkowskiand Gilmour, 2001). Do not use theselfing argument in conjunctionwith inBreed or mgs.the inbreeding coefficient for base individuals. This argument generatesthe numerator relationship matrix for inbred lines. Each cross isassumed to be selfed several times to stabilize as an inbred line as isusual for cereal crops, for example, before being evaluated or crossedwith another line. Since inbreeding is usually associated with strongselection, it is not obvious that a pedigree assumption of covarianceof 0.5 between parent and offspring actually holds. The inBreed argumentcannot be used in conjunction with selfing or mgs.if TRUE, the third identity in the pedigree is the male parent of thefemale parent rather than the female parent (maternal grand-sire).