dim(NeanderMat) [1] 166363 16 summary(NeanderMat) #SNPs #Nea #Ref #Alt Min. : 9.00 Min. : 0.000 Min. : 0.000 Min. : 0.0000 1st Qu.: 9.00 1st Qu.: 6.000 1st Qu.: 5.000 1st Qu.: 0.0000 Median : 10.00 Median : 7.000 Median : 7.000 Median : 0.0000 Mean : 14.47 Mean : 9.586 Mean : 8.595 Mean : 0.8873 3rd Qu.: 14.00 3rd Qu.: 10.000 3rd Qu.: 9.000 3rd Qu.: 1.0000 Max. :266.00 Max. :159.000 Max. :119.000 Max. :100.0000 #New NeaR RefR AltR Min. :0.0000 Min. :0.0000 Min. :0.0000 Min. :0.00000 1st Qu.:0.0000 1st Qu.:0.5556 1st Qu.:0.8750 1st Qu.:0.00000 Median :0.0000 Median :0.6667 Median :1.0000 Median :0.00000 Mean :0.1032 Mean :0.6644 Mean :0.9138 Mean :0.07512 3rd Qu.:0.0000 3rd Qu.:0.7778 3rd Qu.:1.0000 3rd Qu.:0.10000 Max. :6.0000 Max. :1.0000 Max. :1.0000 Max. :1.00000 NewR xAltCon xRefCon mAltCon Min. :0.00000 Min. : 0.0000 Min. : 0.000 Min. : 0.0000 1st Qu.:0.00000 1st Qu.: 0.0000 1st Qu.: 1.000 1st Qu.: 0.0000 Median :0.00000 Median : 0.0000 Median : 1.000 Median : 0.0000 Mean :0.01077 Mean : 0.3952 Mean : 1.038 Mean : 0.4281 3rd Qu.:0.00000 3rd Qu.: 0.0000 3rd Qu.: 1.000 3rd Qu.: 0.0000 Max. :1.00000 Max. :80.0000 Max. :13.000 Max. :80.0000 mRefCon NeaPosC AltPosC RefPosC Min. : 0.00 Min. : 7.0 Min. : 0.0 Min. : 0 1st Qu.: 1.00 1st Qu.: 984.2 1st Qu.: 0.0 1st Qu.: 1420 Median : 1.00 Median : 1493.5 Median : 0.0 Median : 2326 Mean : 1.09 Mean : 1635.3 Mean : 773.6 Mean : 2957 3rd Qu.: 1.00 3rd Qu.: 2130.0 3rd Qu.: 0.0 3rd Qu.: 3663 Max. :13.00 Max. :39758.0 Max. :205077.0 Max. :385084 > format(colSums(NeanderMat),scientific=FALSE) number SNPs number determined in Neandertal "3178092.0000" "2124116.0000" ratio determined ratio reference " 141122.8269" " 189144.8677" ratio alternative ratio new bases " 32166.1156" " 935.0167" oo <- which(NeanderMat[,8]==1.0) perf <- NeanderMat[oo,1:4] perf oo1 <- which(NeanderMat[,4]>40) perf1 <- NeanderMat[oo1,1:4] perf1 NeanderMat[oo1,] #SNPs #Nea #Ref #Alt #New NeaR RefR AltR NewR [1,] 212 128 51 76 1 0.6037736 0.3984375 0.5937500 0.007812500 [2,] 233 136 42 94 0 0.5836910 0.3088235 0.6911765 0.000000000 [3,] 144 75 31 44 0 0.5208333 0.4133333 0.5866667 0.000000000 [4,] 266 157 59 97 1 0.5902256 0.3757962 0.6178344 0.006369427 [5,] 257 159 58 100 1 0.6186770 0.3647799 0.6289308 0.006289308 [6,] 258 149 50 99 0 0.5775194 0.3355705 0.6644295 0.000000000 [7,] 150 107 52 54 1 0.7133333 0.4859813 0.5046729 0.009345794 [8,] 123 85 37 48 0 0.6910569 0.4352941 0.5647059 0.000000000 [9,] 145 91 40 50 1 0.6275862 0.4395604 0.5494505 0.010989011 [10,] 144 120 77 41 2 0.8333333 0.6416667 0.3416667 0.016666667 [11,] 128 84 23 59 2 0.6562500 0.2738095 0.7023810 0.023809524 [12,] 184 112 53 57 2 0.6086957 0.4732143 0.5089286 0.017857143 [13,] 160 102 42 59 1 0.6375000 0.4117647 0.5784314 0.009803922 [14,] 175 111 51 58 2 0.6342857 0.4594595 0.5225225 0.018018018 [15,] 87 68 16 51 1 0.7816092 0.2352941 0.7500000 0.014705882 [16,] 87 68 16 51 1 0.7816092 0.2352941 0.7500000 0.014705882 [17,] 131 101 47 54 0 0.7709924 0.4653465 0.5346535 0.000000000 [18,] 157 110 66 43 1 0.7006369 0.6000000 0.3909091 0.009090909 [19,] 139 96 52 44 0 0.6906475 0.5416667 0.4583333 0.000000000 [20,] 150 110 53 57 0 0.7333333 0.4818182 0.5181818 0.000000000 [21,] 125 96 29 66 1 0.7680000 0.3020833 0.6875000 0.010416667 [22,] 149 112 39 71 2 0.7516779 0.3482143 0.6339286 0.017857143 [23,] 139 96 52 44 0 0.6906475 0.5416667 0.4583333 0.000000000 [24,] 149 109 52 57 0 0.7315436 0.4770642 0.5229358 0.000000000 [25,] 114 87 35 52 0 0.7631579 0.4022989 0.5977011 0.000000000 [26,] 82 54 13 41 0 0.6585366 0.2407407 0.7592593 0.000000000 [27,] 140 92 26 66 0 0.6571429 0.2826087 0.7173913 0.000000000 [28,] 140 92 26 66 0 0.6571429 0.2826087 0.7173913 0.000000000 [29,] 171 118 71 45 2 0.6900585 0.6016949 0.3813559 0.016949153 [30,] 106 73 22 50 1 0.6886792 0.3013699 0.6849315 0.013698630 [31,] 101 73 19 54 0 0.7227723 0.2602740 0.7397260 0.000000000 [32,] 164 110 52 55 3 0.6707317 0.4727273 0.5000000 0.027272727 [33,] 122 80 37 41 2 0.6557377 0.4625000 0.5125000 0.025000000 [34,] 109 72 30 41 1 0.6605505 0.4166667 0.5694444 0.013888889 [35,] 103 75 24 51 0 0.7281553 0.3200000 0.6800000 0.000000000 [36,] 116 77 35 41 1 0.6637931 0.4545455 0.5324675 0.012987013 [37,] 112 64 23 41 0 0.5714286 0.3593750 0.6406250 0.000000000 [38,] 129 78 17 61 0 0.6046512 0.2179487 0.7820513 0.000000000 [39,] 113 72 15 56 1 0.6371681 0.2083333 0.7777778 0.013888889 [40,] 97 57 14 42 1 0.5876289 0.2456140 0.7368421 0.017543860 [41,] 113 72 15 56 1 0.6371681 0.2083333 0.7777778 0.013888889 [42,] 108 54 13 41 0 0.5000000 0.2407407 0.7592593 0.000000000 [43,] 254 144 54 90 0 0.5669291 0.3750000 0.6250000 0.000000000 [44,] 102 69 25 44 0 0.6764706 0.3623188 0.6376812 0.000000000 [45,] 96 64 18 46 0 0.6666667 0.2812500 0.7187500 0.000000000 [46,] 111 73 25 47 1 0.6576577 0.3424658 0.6438356 0.013698630 [47,] 264 151 62 89 0 0.5719697 0.4105960 0.5894040 0.000000000 [48,] 118 77 30 47 0 0.6525424 0.3896104 0.6103896 0.000000000 [49,] 104 73 24 49 0 0.7019231 0.3287671 0.6712329 0.000000000 [50,] 86 63 15 48 0 0.7325581 0.2380952 0.7619048 0.000000000 [51,] 80 60 18 42 0 0.7500000 0.3000000 0.7000000 0.000000000 [52,] 80 58 15 43 0 0.7250000 0.2586207 0.7413793 0.000000000 [53,] 80 58 15 43 0 0.7250000 0.2586207 0.7413793 0.000000000 xAltCon xRefCon mAltCon mRefCon NeaPosC AltPosC RefPosC [1,] 1.0 1.0 1.680000 2.400000 27.0 42.0 65.5 [2,] 1.0 2.0 1.408602 3.292683 18.0 28.0 74.0 [3,] 1.0 1.0 1.534884 2.466667 16.0 38.0 94.5 [4,] 1.0 1.0 1.562500 2.672414 21.0 30.5 72.0 [5,] 1.0 1.0 1.585859 2.649123 22.0 35.0 70.0 [6,] 1.0 2.0 1.489796 3.000000 19.0 31.0 102.0 [7,] 1.0 1.0 1.943396 2.039216 142.0 515.0 301.0 [8,] 1.0 1.0 1.787234 2.194444 141.0 510.0 288.0 [9,] 1.0 2.0 1.795918 2.256410 150.0 372.0 532.0 [10,] 2.5 1.0 2.825000 1.539474 130.0 450.0 236.0 [11,] 1.0 3.0 1.379310 3.636364 185.0 417.5 886.0 [12,] 1.0 1.0 1.571429 2.096154 66.0 113.5 334.0 [13,] 1.0 1.0 1.689655 2.414634 55.0 119.5 259.0 [14,] 1.0 1.0 1.701754 2.140000 63.5 115.0 298.0 [15,] 1.0 4.0 1.280000 4.400000 309.5 652.5 2907.0 [16,] 1.0 4.0 1.280000 4.400000 309.5 652.5 2907.0 [17,] 1.0 1.0 1.867925 2.152174 192.5 312.0 827.5 [18,] 2.0 1.0 2.523810 1.646154 288.0 963.0 748.0 [19,] 2.0 1.0 2.162791 1.843137 357.0 866.0 875.0 [20,] 1.0 1.0 1.839286 2.096154 118.0 260.5 343.0 [21,] 1.0 2.0 1.430769 3.285714 185.5 312.0 827.5 [22,] 1.0 2.0 1.500000 2.842105 192.5 357.5 770.0 [23,] 2.0 1.0 2.162791 1.843137 357.0 866.0 875.0 [24,] 1.0 1.0 1.839286 2.117647 118.5 260.5 344.0 [25,] 1.0 2.0 1.647059 2.529412 166.0 304.0 546.0 [26,] 1.0 2.5 1.300000 4.333333 138.0 263.5 1279.0 [27,] 1.0 2.0 1.369231 3.600000 121.0 285.0 725.0 [28,] 1.0 2.0 1.369231 3.600000 121.0 285.0 725.0 [29,] 1.5 1.0 2.227273 1.642857 89.5 301.0 236.0 [30,] 1.0 2.0 1.448980 2.952381 234.0 528.0 930.0 [31,] 1.0 2.5 1.339623 3.888889 268.0 600.0 979.5 [32,] 1.0 1.0 1.944444 2.019608 174.0 433.0 483.0 [33,] 1.0 1.0 1.725000 2.138889 176.0 367.0 726.5 [34,] 1.0 2.0 1.700000 2.379310 306.0 769.5 1110.0 [35,] 1.0 3.0 1.420000 3.173913 331.5 701.5 1149.0 [36,] 1.0 1.0 1.750000 2.176471 268.0 769.5 832.0 [37,] 1.0 2.0 1.525000 2.772727 101.0 170.5 443.0 [38,] 1.0 2.5 1.266667 4.375000 125.5 229.0 918.0 [39,] 1.0 4.0 1.272727 4.785714 150.0 262.0 1126.0 [40,] 1.0 3.0 1.317073 4.076923 163.5 260.0 1508.0 [41,] 1.0 4.0 1.272727 4.785714 150.0 262.0 1126.0 [42,] 1.0 2.5 1.300000 4.333333 213.0 360.0 1976.0 [43,] 1.0 2.0 1.584270 2.660377 87.0 336.0 349.0 [44,] 1.0 1.0 1.581395 2.333333 157.0 373.0 505.5 [45,] 1.0 3.0 1.355556 3.117647 217.0 375.0 517.0 [46,] 1.0 2.0 1.521739 2.833333 129.0 333.5 661.0 [47,] 1.0 2.0 1.681818 2.426230 87.0 343.0 349.0 [48,] 1.0 1.0 1.652174 2.482759 126.0 374.0 517.0 [49,] 1.0 1.0 1.395833 3.086957 197.0 287.5 998.0 [50,] 1.0 2.5 1.319149 3.785714 164.0 270.0 1643.5 [51,] 1.0 4.0 1.414634 3.411765 354.0 489.0 2543.0 [52,] 1.0 1.5 1.357143 3.428571 117.0 256.5 349.5 [53,] 1.0 1.5 1.357143 3.428571 117.0 256.5 349.5 >