This function calculates pairwise string hamming distances.

hamming(X, Y)

Arguments

X

DNAStringSet

Y

DNAStringSet

References

Vara C et al. (2019) PRDM9 Diveristy at Fine Geographical Scale Reveals Contrasting Evolutionary Patterns and Functional Constraints in Natural Populations of House Mice. Molecular Biology and Evolution, 36(8), 1686-1700.

Author

Kristian K Ullrich

Examples

##load example sequence data
data("mousePRDM9", package="repeatR")
myRepPattern<-"PY"
myRepLength<-84
mousePRDM9.random<-sample(mousePRDM9, 20)
mousePRDM9.random.split<-repeatR::splitRepByPattern(mousePRDM9.random,
    myRepPattern, myRepLength)
##calculate hamming distance
repeatR::hamming(mousePRDM9.random.split$cds[[1]],
    mousePRDM9.random.split$cds[[2]])
#>                                     MK848148.1_cds_QCI31726.1_1_1_84
#> MK848093.1_cds_QCI31671.1_1_1_84                                   3
#> MK848093.1_cds_QCI31671.1_1_85_168                                 0
#> MK848093.1_cds_QCI31671.1_1_169_252                                0
#> MK848093.1_cds_QCI31671.1_1_253_336                                3
#> MK848093.1_cds_QCI31671.1_1_337_420                                2
#> MK848093.1_cds_QCI31671.1_1_421_504                                0
#> MK848093.1_cds_QCI31671.1_1_505_588                                3
#> MK848093.1_cds_QCI31671.1_1_589_672                                1
#> MK848093.1_cds_QCI31671.1_1_673_756                                5
#>                                     MK848148.1_cds_QCI31726.1_1_85_168
#> MK848093.1_cds_QCI31671.1_1_1_84                                     4
#> MK848093.1_cds_QCI31671.1_1_85_168                                   1
#> MK848093.1_cds_QCI31671.1_1_169_252                                  1
#> MK848093.1_cds_QCI31671.1_1_253_336                                  2
#> MK848093.1_cds_QCI31671.1_1_337_420                                  3
#> MK848093.1_cds_QCI31671.1_1_421_504                                  1
#> MK848093.1_cds_QCI31671.1_1_505_588                                  2
#> MK848093.1_cds_QCI31671.1_1_589_672                                  2
#> MK848093.1_cds_QCI31671.1_1_673_756                                  6
#>                                     MK848148.1_cds_QCI31726.1_1_169_252
#> MK848093.1_cds_QCI31671.1_1_1_84                                      0
#> MK848093.1_cds_QCI31671.1_1_85_168                                    3
#> MK848093.1_cds_QCI31671.1_1_169_252                                   3
#> MK848093.1_cds_QCI31671.1_1_253_336                                   4
#> MK848093.1_cds_QCI31671.1_1_337_420                                   1
#> MK848093.1_cds_QCI31671.1_1_421_504                                   3
#> MK848093.1_cds_QCI31671.1_1_505_588                                   3
#> MK848093.1_cds_QCI31671.1_1_589_672                                   3
#> MK848093.1_cds_QCI31671.1_1_673_756                                   6
#>                                     MK848148.1_cds_QCI31726.1_1_253_336
#> MK848093.1_cds_QCI31671.1_1_1_84                                      4
#> MK848093.1_cds_QCI31671.1_1_85_168                                    3
#> MK848093.1_cds_QCI31671.1_1_169_252                                   3
#> MK848093.1_cds_QCI31671.1_1_253_336                                   0
#> MK848093.1_cds_QCI31671.1_1_337_420                                   3
#> MK848093.1_cds_QCI31671.1_1_421_504                                   3
#> MK848093.1_cds_QCI31671.1_1_505_588                                   2
#> MK848093.1_cds_QCI31671.1_1_589_672                                   4
#> MK848093.1_cds_QCI31671.1_1_673_756                                   6
#>                                     MK848148.1_cds_QCI31726.1_1_337_420
#> MK848093.1_cds_QCI31671.1_1_1_84                                      0
#> MK848093.1_cds_QCI31671.1_1_85_168                                    3
#> MK848093.1_cds_QCI31671.1_1_169_252                                   3
#> MK848093.1_cds_QCI31671.1_1_253_336                                   4
#> MK848093.1_cds_QCI31671.1_1_337_420                                   1
#> MK848093.1_cds_QCI31671.1_1_421_504                                   3
#> MK848093.1_cds_QCI31671.1_1_505_588                                   3
#> MK848093.1_cds_QCI31671.1_1_589_672                                   3
#> MK848093.1_cds_QCI31671.1_1_673_756                                   6
#>                                     MK848148.1_cds_QCI31726.1_1_421_504
#> MK848093.1_cds_QCI31671.1_1_1_84                                      2
#> MK848093.1_cds_QCI31671.1_1_85_168                                    1
#> MK848093.1_cds_QCI31671.1_1_169_252                                   1
#> MK848093.1_cds_QCI31671.1_1_253_336                                   2
#> MK848093.1_cds_QCI31671.1_1_337_420                                   1
#> MK848093.1_cds_QCI31671.1_1_421_504                                   1
#> MK848093.1_cds_QCI31671.1_1_505_588                                   2
#> MK848093.1_cds_QCI31671.1_1_589_672                                   2
#> MK848093.1_cds_QCI31671.1_1_673_756                                   4
#>                                     MK848148.1_cds_QCI31726.1_1_505_588
#> MK848093.1_cds_QCI31671.1_1_1_84                                      2
#> MK848093.1_cds_QCI31671.1_1_85_168                                    1
#> MK848093.1_cds_QCI31671.1_1_169_252                                   1
#> MK848093.1_cds_QCI31671.1_1_253_336                                   2
#> MK848093.1_cds_QCI31671.1_1_337_420                                   1
#> MK848093.1_cds_QCI31671.1_1_421_504                                   1
#> MK848093.1_cds_QCI31671.1_1_505_588                                   2
#> MK848093.1_cds_QCI31671.1_1_589_672                                   2
#> MK848093.1_cds_QCI31671.1_1_673_756                                   4
#>                                     MK848148.1_cds_QCI31726.1_1_589_672
#> MK848093.1_cds_QCI31671.1_1_1_84                                      3
#> MK848093.1_cds_QCI31671.1_1_85_168                                    0
#> MK848093.1_cds_QCI31671.1_1_169_252                                   0
#> MK848093.1_cds_QCI31671.1_1_253_336                                   3
#> MK848093.1_cds_QCI31671.1_1_337_420                                   2
#> MK848093.1_cds_QCI31671.1_1_421_504                                   0
#> MK848093.1_cds_QCI31671.1_1_505_588                                   3
#> MK848093.1_cds_QCI31671.1_1_589_672                                   1
#> MK848093.1_cds_QCI31671.1_1_673_756                                   5
#>                                     MK848148.1_cds_QCI31726.1_1_673_756
#> MK848093.1_cds_QCI31671.1_1_1_84                                      0
#> MK848093.1_cds_QCI31671.1_1_85_168                                    3
#> MK848093.1_cds_QCI31671.1_1_169_252                                   3
#> MK848093.1_cds_QCI31671.1_1_253_336                                   4
#> MK848093.1_cds_QCI31671.1_1_337_420                                   1
#> MK848093.1_cds_QCI31671.1_1_421_504                                   3
#> MK848093.1_cds_QCI31671.1_1_505_588                                   3
#> MK848093.1_cds_QCI31671.1_1_589_672                                   3
#> MK848093.1_cds_QCI31671.1_1_673_756                                   6
#>                                     MK848148.1_cds_QCI31726.1_1_757_840
#> MK848093.1_cds_QCI31671.1_1_1_84                                      1
#> MK848093.1_cds_QCI31671.1_1_85_168                                    2
#> MK848093.1_cds_QCI31671.1_1_169_252                                   2
#> MK848093.1_cds_QCI31671.1_1_253_336                                   3
#> MK848093.1_cds_QCI31671.1_1_337_420                                   0
#> MK848093.1_cds_QCI31671.1_1_421_504                                   2
#> MK848093.1_cds_QCI31671.1_1_505_588                                   2
#> MK848093.1_cds_QCI31671.1_1_589_672                                   2
#> MK848093.1_cds_QCI31671.1_1_673_756                                   5
#>                                     MK848148.1_cds_QCI31726.1_1_841_924
#> MK848093.1_cds_QCI31671.1_1_1_84                                      4
#> MK848093.1_cds_QCI31671.1_1_85_168                                    1
#> MK848093.1_cds_QCI31671.1_1_169_252                                   1
#> MK848093.1_cds_QCI31671.1_1_253_336                                   4
#> MK848093.1_cds_QCI31671.1_1_337_420                                   3
#> MK848093.1_cds_QCI31671.1_1_421_504                                   1
#> MK848093.1_cds_QCI31671.1_1_505_588                                   4
#> MK848093.1_cds_QCI31671.1_1_589_672                                   2
#> MK848093.1_cds_QCI31671.1_1_673_756                                   6
#>                                     MK848148.1_cds_QCI31726.1_1_925_1008
#> MK848093.1_cds_QCI31671.1_1_1_84                                       0
#> MK848093.1_cds_QCI31671.1_1_85_168                                     3
#> MK848093.1_cds_QCI31671.1_1_169_252                                    3
#> MK848093.1_cds_QCI31671.1_1_253_336                                    4
#> MK848093.1_cds_QCI31671.1_1_337_420                                    1
#> MK848093.1_cds_QCI31671.1_1_421_504                                    3
#> MK848093.1_cds_QCI31671.1_1_505_588                                    3
#> MK848093.1_cds_QCI31671.1_1_589_672                                    3
#> MK848093.1_cds_QCI31671.1_1_673_756                                    6
#>                                     MK848148.1_cds_QCI31726.1_1_1009_1092
#> MK848093.1_cds_QCI31671.1_1_1_84                                        4
#> MK848093.1_cds_QCI31671.1_1_85_168                                      4
#> MK848093.1_cds_QCI31671.1_1_169_252                                     4
#> MK848093.1_cds_QCI31671.1_1_253_336                                     1
#> MK848093.1_cds_QCI31671.1_1_337_420                                     3
#> MK848093.1_cds_QCI31671.1_1_421_504                                     4
#> MK848093.1_cds_QCI31671.1_1_505_588                                     1
#> MK848093.1_cds_QCI31671.1_1_589_672                                     3
#> MK848093.1_cds_QCI31671.1_1_673_756                                     7
#>                                     MK848148.1_cds_QCI31726.1_1_1093_1176
#> MK848093.1_cds_QCI31671.1_1_1_84                                        3
#> MK848093.1_cds_QCI31671.1_1_85_168                                      1
#> MK848093.1_cds_QCI31671.1_1_169_252                                     1
#> MK848093.1_cds_QCI31671.1_1_253_336                                     4
#> MK848093.1_cds_QCI31671.1_1_337_420                                     2
#> MK848093.1_cds_QCI31671.1_1_421_504                                     1
#> MK848093.1_cds_QCI31671.1_1_505_588                                     2
#> MK848093.1_cds_QCI31671.1_1_589_672                                     0
#> MK848093.1_cds_QCI31671.1_1_673_756                                     6
#>                                     MK848148.1_cds_QCI31726.1_1_1177_1260
#> MK848093.1_cds_QCI31671.1_1_1_84                                        6
#> MK848093.1_cds_QCI31671.1_1_85_168                                      5
#> MK848093.1_cds_QCI31671.1_1_169_252                                     5
#> MK848093.1_cds_QCI31671.1_1_253_336                                     6
#> MK848093.1_cds_QCI31671.1_1_337_420                                     5
#> MK848093.1_cds_QCI31671.1_1_421_504                                     5
#> MK848093.1_cds_QCI31671.1_1_505_588                                     6
#> MK848093.1_cds_QCI31671.1_1_589_672                                     6
#> MK848093.1_cds_QCI31671.1_1_673_756                                     0