This function creates a granthamMatrix object to be used
with the rcpp_distSTRING function. By default,the grantham matrix is
defined as from Grantham 1974.
(see https://link.springer.com/article/10.1007/s00335-017-9704-9)
granthamMatrix()matrix
Grantham R. (1974). Amino Acid Difference Formula to Help Explain Protein Evolution. Science,185(4154),862-864.
granthamMatrix()
#> S R L P T A V G I F Y C H Q N K D E M
#> S 0 110 145 74 58 99 124 56 142 155 144 112 89 68 46 121 65 80 135
#> R 110 0 102 103 71 112 96 125 97 97 77 180 29 43 86 26 96 54 91
#> L 145 102 0 98 92 96 32 138 5 22 36 198 99 113 153 107 172 138 15
#> P 74 103 98 0 38 27 68 42 95 14 110 169 77 76 91 103 108 93 87
#> T 58 71 92 38 0 58 69 59 89 103 92 149 47 42 65 78 85 65 81
#> A 99 112 96 27 58 0 64 60 94 13 112 195 86 91 111 106 126 107 84
#> V 124 96 32 68 69 64 0 109 29 50 55 192 84 96 133 97 152 121 21
#> G 56 125 138 42 59 60 109 0 135 153 147 159 98 87 80 127 94 98 127
#> I 142 97 5 95 89 94 29 135 0 21 33 198 94 109 149 102 168 134 10
#> F 155 97 22 114 103 113 50 153 21 0 22 205 100 116 158 102 177 140 28
#> Y 144 77 36 110 92 112 55 147 33 22 0 194 83 99 143 85 160 122 36
#> C 112 180 198 169 149 195 192 159 198 205 194 0 174 154 139 202 154 170 196
#> H 89 29 99 77 47 86 84 98 94 100 83 174 0 24 68 32 81 40 87
#> Q 68 43 113 76 42 91 96 87 109 116 99 154 24 0 46 53 61 29 101
#> N 46 86 153 91 65 111 133 80 149 158 143 139 68 46 0 94 23 42 142
#> K 121 26 107 103 78 106 97 127 102 102 85 202 32 53 94 0 101 56 95
#> D 65 96 172 108 85 126 152 94 168 177 160 154 81 61 23 101 0 45 160
#> E 80 54 138 93 65 107 121 98 134 140 122 170 40 29 42 56 45 0 126
#> M 135 91 15 87 81 84 21 127 10 28 36 196 87 101 142 95 160 126 0
#> W 177 101 61 147 128 148 88 184 61 40 37 215 115 130 174 110 181 152 67
#> . -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
#> - -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
#> X -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1
#> W . - X
#> S 177 -1 -1 -1
#> R 101 -1 -1 -1
#> L 61 -1 -1 -1
#> P 147 -1 -1 -1
#> T 128 -1 -1 -1
#> A 148 -1 -1 -1
#> V 88 -1 -1 -1
#> G 184 -1 -1 -1
#> I 61 -1 -1 -1
#> F 40 -1 -1 -1
#> Y 37 -1 -1 -1
#> C 215 -1 -1 -1
#> H 115 -1 -1 -1
#> Q 130 -1 -1 -1
#> N 174 -1 -1 -1
#> K 110 -1 -1 -1
#> D 181 -1 -1 -1
#> E 152 -1 -1 -1
#> M 67 -1 -1 -1
#> W 0 -1 -1 -1
#> . -1 -1 -1 -1
#> - -1 -1 -1 -1
#> X -1 -1 -1 -1