Hamming distance is calculated as the number of base differences between two sequences which can be expressed as a count or a proportion. Typically, it is calculated between two sequences of equal length. In the context of DArT trimmed sequences, which differ in length but which are anchored to the left by the restriction enzyme recognition sequence, it is sensible to compare the two trimmed sequences starting from immediately after the common recognition sequence and terminating at the last base of the shorter sequence.
gl.report.hamming(gl, rs = 5)-- genlight object [required]
-- number of bases in the restriction enzyme recognition sequence [default = 4]
Histogram of Hamming distance for the gl object
Hamming distance can be computed by exploiting the fact that the dot product of two binary vectors x and (1-y) counts the corresponding elements that are different between x and y. This approach can also be used for vectors that contain more than two possible values at each position (e.g. A, C, T or G).
If a pair of DNA sequences are of differing length, the longer is truncated.
The algorithm is that of Johann de Jong https://johanndejong.wordpress.com/2015/10/02/faster-hamming-distance-in-r-2/ as implimented in utils.hamming.r
# NOT RUN {
gl.report.hamming(testset.gl)
# }
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