ASReml-S reference manual - VSN International

5.2 Pedigree, G-inverse objects and genetic groups 55• three columns: the identity of the individual, its male parent and its female parent(or maternal grand sire if the MGS option to asreml.Ainverse() is to be specified),• is sorted so that the row giving the pedigree of an individual appears before any rowwhere that individual appears as a parent,• uses identity 0 or NA for unknown parentsFor example, the first 20 lines of harvey.ped are:> harvey.ped harvey.ped[1:20,]Calf Sire Dam1 Sire_1 0 02 Sire_2 0 03 Sire_3 0 04 Sire_4 0 05 Sire_5 0 06 Sire_6 0 07 Sire_7 0 08 Sire_8 0 09 Sire_9 0 010 101 Sire_1 011 102 Sire_1 012 103 Sire_1 013 104 Sire_1 014 105 Sire_1 015 106 Sire_1 016 107 Sire_1 017 108 Sire_1 018 109 Sire_2 019 110 Sire_2 020 111 Sire_2 05.2.2 giv objectsAn inverse relationship matrix, A −1 or a general inverse matrix from an external sourcecan be included in the analysis as:• a data frame of three columns containing the non-zero elements of the lower triangleof the matrix in row order. The first two columns of the data frame are the row andcolumn indices and must be named row and column, respectively. This is the structurereturned by asreml.Ainverse().• a matrix object. Only the lower triangle is used and NAs are ignored.• the complete lower triangle in vector form stored row by row; NAs are ignored.• in all cases every diagonal element must be present.In all cases the giv matrix object must have an attribute rowNames, a character vectorthat uniquely identifies each row of the matrix. This vector of identifiers may be a superset of the vector of levels of the corresponding factor in the data, but must at leastcontain all the individuals in the data.An inverse relationship matrix can be obtained from the harvey pedigree using:> harvey.ainv