Integer Rank Codes for Haplotypes
Create a vector of integer codes for the input matrix of haplotypes. The haplotypes in the input matrix are converted to character strings, and if there are C unique strings, the integer codes for the haplotypes will be 1, 2, ..., C.
A matrix of haplotypes. If there are N haplotypes for K loci, hap have dimensions N x K.
The alleles that make up each row in hap are pasted together as character strings, and the unique strings are sorted so that the rank order of the sorted strings is used as the integer code for the unique haplotypes.
List with elements:
Vector of integer codes for the input data (hap). The value of hash is the row number of the unique haplotypes given in the returned matrix hap.mtx.
Matrix of unique haplotypes.
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