HIBLUP currently only accept Relationship Matrix (XRM) in binary format, which has the most efficiency of file writing and data loading, and costs the least usage of disk space, e.g.
*.id has one column listing the id of all individuals, the file
*.bin store the lower triangle elements of the XRM for dense matrix, and the file
*.sparse.bin store the row index, column index, and triangle elements of the XRM for sparse matrix.
By default, those files is generated by
--make-xrm in HIBLUP (see Construct relationship matrix).
Additionally, we have developed a file format converter for making binary relationship matrix, please refer to corresponding section (see Format conversion of XRM). To use the binary XRM by HIBLUP, just assign its prefix to the option
./hiblup ... --xrm demo.GA ...
If there are more than one XRMs, please use comma as separator between prefix:
./hiblup ... --xrm demo.GA,demo.GD ...
HIBLUP has the function of computing the inverse of XRM, which maybe useful for other software (e.g. BLUPF90, DMU, ASReml, …), but it’s useless for HIBLUP, as HIBLUP uses XRM directly to estimate variance components or solve mixed model equation, therefore please do not assign an inverse of relationship matrix to HIBLUP, unless you know what you are doing.