This function calculates pairwise string hamming distances.
hamming(X, Y)
DNAStringSet
DNAStringSet
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.
##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