GeneMatrix

This package is iniatially contended for the constructions various matrices used in animal breeding and genetics. It also provides a set of file I/O functions to store and retrieve the matrices to and from a storage, e.g, HDD. The reason for the latter is that saving the matrix might occupy too much disk space, e.g., the 3-column, row-column-value storage. It also prevents precision loss while store float number in text format.

File I/O

The storage format is called XY format. Each contains a header, as defined by struct xyheader. The starting 3 characters of a header are "XY ". The 4th character is any one of "FLUS", that is Full matrix, Lower triangle, Upper triangle, or lower triangle of a Symmetric matrix. the 5th character specify if the genotypes matrix is of nLoci $\times$ nID (N), or Transposed if applies. The 6th character specify element types of the matrix. The currently supported types are Bool, Int8, Int16, Int32, Int64, Int128, UInt8, UInt16, UInt32, UInt64, UInt128, Float16, Float32, Float64, though some of them may never be used. If a new type is to be added, it must appended to the end of above.

I/O functions

The function for reading is readxy. It only take one argument of file name. The one for writing is writexy(file, mat; mattp = 'F', trans = 'N'). It write matrix mat into file. If mat is symmetric, then mattp is overruled as S.

The package also provides two other I/O functions to input and output plink bed files.

• To be added

Matrix construction

Numerical relationship matrix related

Genome relationship matrix related

Pedigree

Compact genotype storage and manipulation methods

Todo

• nrm: numerical relationship matrix
• nrminv: the inverse of nrm
• codeped, recode pedigree to 1:nID.
• readmacs, read simulation results from MaCS.
• bed2int8, convert bed file formats to Int8