load(file=paste("DenisovaMat.Rda",sep="")) load(file=paste("NeanderMat.Rda",sep="")) load(file=paste("AncestMat.Rda",sep="")) load(file=paste("PopulationMat.Rda",sep="")) load(file="SubPopulationMat.Rda") load(file="SubPopCorMat.Rda") library(fabia) library(hapFabia) load("dups.Rda") load("analyzeResult.Rda") source("plotAncientGenomes.R") shiftSize <- 5000 segmentSize <- 10000 fileName="KPGP1000_chr1" # without type de <- which(DenisovaMat[,12]>0.3) denis <- which(DenisovaMat[,12]>0.8) SubPopCorMat[denis,3:5] kor <- which(SubPopCorMat[,16]>0.9) > korA1 <- which(SubPopCorMat[,16]>0.2) > korA2 <- which(SubPopCorMat[,16]<0.8) > korA <- intersect(korA1,korA2) SubPopCorMat[korA,3:5] posAll <- 342 ibdC <- 62 posAll <- 341 ibdC <- 131 posAll <- 231 ibdC <- 192 start <- (posAll-1)*shiftSize end <- start + segmentSize pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste(fileName,pRange,"_resAnno",".Rda",sep="")) IBD <- resHapFabia$mergedIBD plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) name="korDenis3" pdf(paste(name,".pdf",sep=""),width=12) plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) dev.off() denis <- which(DenisovaMat[,12]>0.8) denis <- which(SubPopCorMat[,16]>0.95) devAskNewPage(ask=TRUE) lde <- length(denis) for (i in 1:lde) { posAll <- SubPopCorMat[denis[i],4] ibdC <- SubPopCorMat[denis[i],3] start <- (posAll-1)*shiftSize end <- start + segmentSize pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste(fileName,pRange,"_resAnno",".Rda",sep="")) IBD <- resHapFabia$mergedIBD message("Haplotype: ",i," out of ",lde) plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) } devAskNewPage(ask=FALSE) No. 13 SNPs: 11 Samples: 3 [1] 1058 1204 1234 1308 ibdC posAll [1,] 201 341 [2,] 146 367 [3,] 155 435 [4,] 155 621 posAll <- 621 ibdC <- 155 start <- (posAll-1)*shiftSize end <- start + segmentSize pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste(fileName,pRange,"_resAnno",".Rda",sep="")) IBD <- resHapFabia$mergedIBD plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) name="korK12" pdf(paste(name,".pdf",sep=""),width=12) plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotAncientGenomes(IBD,filename=paste(fileName,pRange,"_mat",sep=""),ibdC) dev.off() pos snps samples K1: (5,70) 2,074,869 14 5 (twins 6->8) K2: (5,72) 2,199,035 17 3 (twins 90-91) K3: (22,81) 7,450,961 19 5 (twins 90-91 neander+denis) K4: (27,137) 9,114,317 21 5 (both twins) K5: (50,16) 17,266,458 51 34 (???typical korean - kpgp10 and kpgp11 not!) K6: (72,43) 24,314,901 175 30 (???typical korean kpgp10 not) K7: (87,208) 30,533,854 9 4 (familiy relation 2->5->8) K8: (133,179) 47,262,203 15 9 (familiy relation 1->(3,5,9) 5->7 9->(11,12)) K9: (225,125) 80,861,614 14 3 (twins sequencing errors) K10: (339,125) 121,467,825 10 10 (??? common passt nicht family relation 1->(3,9) 3->4 9->(11,12)) K11: (341,138) 144,536,579 89 5 (caucasian 10 to childs 11 and 12) K12: (621,155) 245,571,656 11 3 (twin, denisova) popS <- SubPopulationMat[denis,] dS <- DenisovaMat[denis,] ine <- rbind(c(10,20),c(14,5),c(17,3),c(19,5),c(21,5),c(51,34),c(175,30),c(9,4),c(15,9),c(14,3),c(10,10),c(89,5),c(11,3)) for (i in 1:dim(ine)[1]) { w1 <- which(popS[,5]==ine[i,2]) w2 <- which(dS[,5]==ine[i,1]) message("No. ",i," SNPs: ",ine[i,1]," Samples: ",ine[i,2]) iww <- intersect(w1,w2) print(iww) print(popS[iww,3:4]) } > colnames(SubPopCorMat) [1] "allCount1" "allCount" "ibdC" "posAll" "#Samples" "ASW" [7] "CEU" "CEUKOR" "CHB" "CHS" "CLM" "FIN" [13] "GBR" "IBS" "JPT" "KOR" "KORdup" "LWK" [19] "MXL" "PUR" "TSI" "YRI" > colnames(DenisovaMat) [1] "allCount1" "allCount" "ibdC" "posAll" "#SNPs" "#Nea" [7] "#Ref" "#Alt" "#New" "NeaR" "RefR" "AltR" [13] "NewR" "xAltCon" "xRefCon" "mAltCon" "mRefCon" "NeaPosC" [19] "AltPosC" "RefPosC" ab <- which(AncestMat[,8]>30) AncestMat[ab[140:180],] ab <- which(DenisovaMat[,8]>10) DenisovaMat[ab[240:280],] ab <- which(NeanderMat[,8]>30) NeanderMat[ab,] posAll <- 16 ibdC <- 222 #denisS1: posAll <- 95 ibdC <- 4 #denisS2: posAll <- 384 ibdC <- 80 posAll <- 131 ibdC <- 62 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="denisS2" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ################### de <- which(DenisovaMat[,12]>0.3) AFR1 <- which(PopulationMat[,6]>0.2) ASN1 <- which(PopulationMat[,8]>0.2) deASN <- intersect(ASN1,de) deANSAFR <- intersect(deASN,AFR1) du <- which(DenisovaMat[,5]>30) duANSAFR <- intersect(du,deANSAFR) > DenisovaMat[duANSAFR,3:10] ibdC posAll #SNPs #Nea #Ref #Alt #New NeaR [1,] 69 21 42 42 26 15 1 1.0000000 [2,] 96 28 37 37 21 15 1 1.0000000 [3,] 256 28 36 36 23 13 0 1.0000000 [4,] 8 29 111 111 51 60 0 1.0000000 [5,] 10 29 86 86 42 44 0 1.0000000 [6,] 74 29 42 42 25 17 0 1.0000000 [7,] 7 30 56 56 31 25 0 1.0000000 [8,] 68 31 73 73 41 31 1 1.0000000 [9,] 228 31 51 51 27 24 0 1.0000000 [10,] 33 32 64 64 33 30 1 1.0000000 [11,] 216 32 52 52 28 24 0 1.0000000 [12,] 191 39 100 100 36 64 0 1.0000000 [13,] 56 43 75 74 40 33 1 0.9866667 [14,] 57 43 117 117 72 44 1 1.0000000 [15,] 94 43 100 99 42 56 1 0.9900000 [16,] 18 44 144 143 80 61 2 0.9930556 [17,] 73 44 79 78 44 33 1 0.9873418 [18,] 61 45 57 57 20 37 0 1.0000000 [19,] 55 46 70 70 33 37 0 1.0000000 [20,] 1 59 34 34 17 17 0 1.0000000 [21,] 78 67 57 57 38 19 0 1.0000000 [22,] 13 84 72 72 38 34 0 1.0000000 [23,] 61 85 33 33 15 18 0 1.0000000 [24,] 78 85 76 76 42 34 0 1.0000000 [25,] 70 86 61 61 32 29 0 1.0000000 [26,] 71 86 61 61 33 28 0 1.0000000 [27,] 83 86 38 38 15 23 0 1.0000000 [28,] 35 87 59 59 38 21 0 1.0000000 [29,] 50 87 76 76 46 30 0 1.0000000 [30,] 40 91 61 61 28 33 0 1.0000000 [31,] 41 91 62 62 30 32 0 1.0000000 [32,] 3 92 71 71 37 34 0 1.0000000 [33,] 25 92 96 96 54 42 0 1.0000000 [34,] 63 92 71 71 39 32 0 1.0000000 [35,] 35 93 95 95 53 39 3 1.0000000 [36,] 206 93 104 104 70 32 2 1.0000000 [37,] 42 94 83 83 47 36 0 1.0000000 [38,] 4 95 82 82 46 36 0 1.0000000 [39,] 43 97 81 81 55 26 0 1.0000000 [40,] 10 98 40 40 27 13 0 1.0000000 [41,] 225 98 72 72 47 25 0 1.0000000 [42,] 22 99 55 55 36 19 0 1.0000000 [43,] 8 100 66 66 44 22 0 1.0000000 [44,] 18 101 135 135 88 46 1 1.0000000 [45,] 141 101 40 40 23 17 0 1.0000000 [46,] 249 101 125 125 81 42 2 1.0000000 [47,] 59 102 98 98 57 40 1 1.0000000 [48,] 74 122 39 39 16 23 0 1.0000000 [49,] 47 123 55 55 27 28 0 1.0000000 [50,] 136 127 36 36 15 21 0 1.0000000 [51,] 17 130 59 59 20 38 1 1.0000000 [52,] 142 130 40 40 6 34 0 1.0000000 [53,] 39 131 116 116 47 68 1 1.0000000 [54,] 57 131 131 131 41 90 0 1.0000000 [55,] 60 131 157 157 69 88 0 1.0000000 [56,] 61 131 139 139 49 90 0 1.0000000 [57,] 62 131 150 150 46 102 2 1.0000000 [58,] 1 132 42 42 21 21 0 1.0000000 [59,] 44 132 73 73 13 60 0 1.0000000 [60,] 46 132 149 149 45 102 2 1.0000000 [61,] 55 132 94 94 47 47 0 1.0000000 [62,] 215 132 114 114 30 84 0 1.0000000 [63,] 237 132 101 101 41 60 0 1.0000000 [64,] 58 133 48 48 30 18 0 1.0000000 [65,] 32 134 51 51 33 18 0 1.0000000 [66,] 46 145 44 44 26 18 0 1.0000000 [67,] 47 145 55 55 36 18 1 1.0000000 [68,] 91 145 69 69 47 22 0 1.0000000 [69,] 92 145 58 58 25 33 0 1.0000000 [70,] 3 146 68 68 35 33 0 1.0000000 [71,] 39 146 53 53 31 22 0 1.0000000 [72,] 12 170 116 116 64 52 0 1.0000000 [73,] 13 170 63 63 38 25 0 1.0000000 [74,] 60 170 106 106 70 36 0 1.0000000 [75,] 13 171 108 108 72 36 0 1.0000000 [76,] 14 171 50 50 33 17 0 1.0000000 [77,] 108 171 76 76 24 52 0 1.0000000 [78,] 178 171 38 38 22 16 0 1.0000000 [79,] 61 174 39 39 19 19 1 1.0000000 [80,] 44 203 61 61 40 20 1 1.0000000 [81,] 81 204 62 62 40 21 1 1.0000000 [82,] 17 225 51 51 18 31 2 1.0000000 [83,] 1 226 46 46 32 14 0 1.0000000 [84,] 57 226 43 43 14 28 1 1.0000000 [85,] 59 227 43 43 27 16 0 1.0000000 [86,] 18 229 100 100 60 39 1 1.0000000 [87,] 56 229 118 118 46 69 3 1.0000000 [88,] 269 229 93 93 32 60 1 1.0000000 [89,] 9 230 125 125 55 67 3 1.0000000 [90,] 16 231 91 91 44 47 0 1.0000000 [91,] 248 231 69 69 29 40 0 1.0000000 [92,] 3 232 101 101 52 49 0 1.0000000 [93,] 69 232 56 56 24 32 0 1.0000000 [94,] 42 233 83 83 55 28 0 1.0000000 [95,] 230 233 67 67 45 22 0 1.0000000 [96,] 34 234 42 42 19 23 0 1.0000000 [97,] 89 234 71 71 44 27 0 1.0000000 [98,] 5 244 66 66 39 26 1 1.0000000 [99,] 172 244 66 66 43 22 1 1.0000000 [100,] 23 245 75 75 46 28 1 1.0000000 [101,] 61 251 46 46 31 14 1 1.0000000 [102,] 223 252 45 45 30 14 1 1.0000000 [103,] 42 259 34 34 23 11 0 1.0000000 [104,] 233 268 39 39 23 16 0 1.0000000 [105,] 96 269 35 35 20 15 0 1.0000000 [106,] 39 306 50 50 31 19 0 1.0000000 [107,] 1 307 64 64 43 20 1 1.0000000 [108,] 31 307 56 56 36 20 0 1.0000000 [109,] 59 309 31 31 9 21 1 1.0000000 [110,] 9 335 35 35 7 28 0 1.0000000 [111,] 47 335 37 37 3 34 0 1.0000000 [112,] 114 335 53 53 5 48 0 1.0000000 [113,] 39 348 32 31 20 11 0 0.9687500 [114,] 9 354 66 66 40 26 0 1.0000000 [115,] 97 354 70 70 44 26 0 1.0000000 [116,] 286 354 64 64 31 33 0 1.0000000 [117,] 3 355 38 38 13 25 0 1.0000000 [118,] 48 355 33 33 12 21 0 1.0000000 [119,] 134 355 91 91 53 38 0 1.0000000 [120,] 185 356 32 32 12 20 0 1.0000000 [121,] 201 356 58 58 21 37 0 1.0000000 [122,] 202 356 61 61 15 46 0 1.0000000 [123,] 3 357 82 82 23 58 1 1.0000000 [124,] 10 357 59 59 26 33 0 1.0000000 [125,] 39 358 58 58 25 33 0 1.0000000 [126,] 4 377 109 108 46 62 0 0.9908257 [127,] 5 377 103 103 41 61 1 1.0000000 [128,] 6 377 80 80 49 29 2 1.0000000 [129,] 7 377 62 62 36 25 1 1.0000000 [130,] 29 378 116 115 52 62 1 0.9913793 [131,] 31 378 108 108 44 62 2 1.0000000 [132,] 32 378 93 93 60 31 2 1.0000000 [133,] 33 378 69 69 43 25 1 1.0000000 [134,] 40 383 108 108 71 35 2 1.0000000 [135,] 206 383 79 79 38 39 2 1.0000000 [136,] 8 384 52 52 33 19 0 1.0000000 [137,] 57 384 42 42 20 21 1 1.0000000 [138,] 58 384 57 57 30 26 1 1.0000000 [139,] 80 384 54 54 20 33 1 1.0000000 [140,] 105 384 78 78 33 44 1 1.0000000 [141,] 127 384 111 111 69 40 2 1.0000000 [142,] 3 385 55 55 33 21 1 1.0000000 [143,] 100 385 60 60 33 26 1 1.0000000 [144,] 223 385 42 42 25 17 0 1.0000000 [145,] 57 390 61 61 40 21 0 1.0000000 [146,] 68 390 56 56 35 21 0 1.0000000 [147,] 17 391 64 64 43 21 0 1.0000000 [148,] 31 391 81 81 35 45 1 1.0000000 [149,] 58 391 85 85 45 39 1 1.0000000 [150,] 172 391 38 38 23 15 0 1.0000000 [151,] 31 392 67 67 29 38 0 1.0000000 [152,] 113 392 77 77 31 45 1 1.0000000 [153,] 56 422 34 34 22 11 1 1.0000000 [154,] 233 422 43 43 22 21 0 1.0000000 [155,] 36 449 62 62 42 19 1 1.0000000 [156,] 3 450 56 56 37 19 0 1.0000000 [157,] 120 451 66 66 45 21 0 1.0000000 [158,] 4 470 90 90 39 50 1 1.0000000 [159,] 5 470 100 100 66 32 2 1.0000000 [160,] 146 470 80 80 48 31 1 1.0000000 [161,] 14 471 94 94 43 50 1 1.0000000 [162,] 165 471 90 90 57 32 1 1.0000000 [163,] 152 475 49 49 16 32 1 1.0000000 [164,] 60 503 77 77 22 55 0 1.0000000 [165,] 61 503 77 77 27 50 0 1.0000000 [166,] 16 519 55 55 38 17 0 1.0000000 [167,] 95 519 45 45 25 20 0 1.0000000 [168,] 35 521 48 48 22 26 0 1.0000000 [169,] 39 522 111 111 75 34 2 1.0000000 [170,] 31 538 78 78 42 36 0 1.0000000 [171,] 62 538 105 105 47 58 0 1.0000000 [172,] 63 538 48 48 27 20 1 1.0000000 [173,] 68 538 91 91 44 47 0 1.0000000 [174,] 158 538 100 100 58 41 1 1.0000000 [175,] 159 538 37 37 19 18 0 1.0000000 [176,] 7 539 38 38 25 13 0 1.0000000 [177,] 9 539 89 89 32 57 0 1.0000000 [178,] 10 539 65 65 33 32 0 1.0000000 [179,] 72 539 46 46 27 19 0 1.0000000 [180,] 94 539 67 67 32 34 1 1.0000000 [181,] 39 556 104 104 40 62 2 1.0000000 [182,] 26 557 99 99 39 58 2 1.0000000 [183,] 27 557 86 86 28 57 1 1.0000000 [184,] 109 561 74 74 42 32 0 1.0000000 [185,] 133 561 91 91 56 33 2 1.0000000 [186,] 37 562 92 92 57 33 2 1.0000000 [187,] 75 562 74 74 50 24 0 1.0000000 [188,] 69 563 52 52 34 18 0 1.0000000 [189,] 70 563 110 107 53 53 1 0.9727273 [190,] 3 564 71 69 27 42 0 0.9718310 [191,] 85 564 45 45 27 18 0 1.0000000 [192,] 152 564 94 91 48 42 1 0.9680851 [193,] 4 565 31 31 19 12 0 1.0000000 [194,] 7 565 37 37 22 15 0 1.0000000 [195,] 72 565 68 68 40 26 2 1.0000000 [196,] 87 565 63 63 36 27 0 1.0000000 [197,] 16 566 69 69 41 26 2 1.0000000 [198,] 57 566 36 36 21 15 0 1.0000000 [199,] 66 566 36 36 24 12 0 1.0000000 [200,] 67 566 49 49 20 28 1 1.0000000 [201,] 69 566 51 51 27 23 1 1.0000000 [202,] 70 566 81 81 49 32 0 1.0000000 [203,] 25 567 77 77 43 32 2 1.0000000 [204,] 54 567 34 34 22 12 0 1.0000000 [205,] 55 567 31 31 17 13 1 1.0000000 [206,] 57 567 80 80 48 32 0 1.0000000 [207,] 7 570 63 63 31 32 0 1.0000000 [208,] 38 571 49 49 22 27 0 1.0000000 [209,] 48 571 80 80 40 39 1 1.0000000 [210,] 65 571 37 37 13 24 0 1.0000000 [211,] 259 572 34 34 23 11 0 1.0000000 [212,] 70 573 66 66 44 22 0 1.0000000 [213,] 240 573 41 41 24 17 0 1.0000000 [214,] 18 574 119 119 64 55 0 1.0000000 [215,] 31 574 108 108 56 52 0 1.0000000 [216,] 32 574 101 101 65 36 0 1.0000000 [217,] 36 574 62 62 36 26 0 1.0000000 [218,] 241 574 89 89 44 45 0 1.0000000 [219,] 18 575 57 57 25 31 1 1.0000000 [220,] 56 575 153 153 83 70 0 1.0000000 [221,] 57 575 112 112 59 53 0 1.0000000 [222,] 58 575 101 101 65 36 0 1.0000000 [223,] 238 575 71 71 41 30 0 1.0000000 [224,] 2 576 64 64 29 34 1 1.0000000 [225,] 22 589 104 104 66 37 1 1.0000000 [226,] 9 590 79 79 51 27 1 1.0000000 [227,] 66 590 80 80 43 37 0 1.0000000 [228,] 191 590 64 64 27 37 0 1.0000000 [229,] 37 615 54 54 26 28 0 1.0000000 [230,] 83 615 72 72 43 28 1 1.0000000 [231,] 252 615 31 31 19 12 0 1.0000000 [232,] 19 616 37 37 21 16 0 1.0000000 [233,] 204 616 34 34 17 17 0 1.0000000 > ne <- which(NeanderMat[,12]>0.3) AFR1 <- which(PopulationMat[,6]>0.2) ASN1 <- which(PopulationMat[,8]>0.2) neASN <- intersect(ASN1,ne) neANSAFR <- intersect(neASN,AFR1) nu <- which(NeanderMat[,5]>30) nuANSAFR <- intersect(nu,neANSAFR) NeanderMat[nuANSAFR,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 133 1 32 28 9 19 0.6785714 [2,] 69 21 42 28 7 21 0.7500000 [3,] 8 29 111 74 40 32 0.4324324 [4,] 10 29 86 66 31 35 0.5303030 [5,] 7 30 56 40 19 21 0.5250000 [6,] 68 31 73 52 28 23 0.4423077 [7,] 228 31 51 34 18 16 0.4705882 [8,] 33 32 64 45 22 22 0.4888889 [9,] 216 32 52 34 19 15 0.4411765 [10,] 29 36 55 36 20 16 0.4444444 [11,] 191 39 100 70 32 38 0.5428571 [12,] 46 41 77 50 16 34 0.6800000 [13,] 56 43 75 63 41 21 0.3333333 [14,] 57 43 117 92 59 32 0.3478261 [15,] 94 43 100 90 53 35 0.3888889 [16,] 18 44 144 120 77 41 0.3416667 [17,] 73 44 79 66 45 20 0.3030303 [18,] 61 45 57 41 15 25 0.6097561 [19,] 55 46 70 54 28 25 0.4629630 [20,] 79 46 48 32 17 14 0.4375000 [21,] 59 47 47 31 16 14 0.4516129 [22,] 1 59 34 21 9 11 0.5238095 [23,] 13 84 72 57 29 28 0.4912281 [24,] 61 85 33 24 13 11 0.4583333 [25,] 78 85 76 60 31 28 0.4666667 [26,] 36 93 65 42 25 17 0.4047619 [27,] 6 94 51 32 22 10 0.3125000 [28,] 45 94 58 38 22 16 0.4210526 [29,] 43 97 81 54 37 17 0.3148148 [30,] 10 98 40 28 18 10 0.3571429 [31,] 225 98 72 47 32 15 0.3191489 [32,] 22 99 55 41 25 16 0.3902439 [33,] 8 100 66 48 31 17 0.3541667 [34,] 74 122 39 30 17 13 0.4333333 [35,] 47 123 55 41 17 23 0.5609756 [36,] 136 127 36 26 12 14 0.5384615 [37,] 17 130 59 38 18 20 0.5263158 [38,] 142 130 40 28 9 19 0.6785714 [39,] 39 131 116 75 42 33 0.4400000 [40,] 57 131 131 101 47 54 0.5346535 [41,] 60 131 157 110 66 43 0.3909091 [42,] 61 131 139 96 52 44 0.4583333 [43,] 62 131 150 110 53 57 0.5181818 [44,] 1 132 42 32 20 12 0.3750000 [45,] 44 132 73 47 20 27 0.5744681 [46,] 46 132 149 109 52 57 0.5229358 [47,] 55 132 94 63 40 22 0.3492063 [48,] 215 132 114 87 35 52 0.5977011 [49,] 237 132 101 74 42 31 0.4189189 [50,] 58 133 48 29 18 10 0.3448276 [51,] 32 134 51 28 18 9 0.3214286 [52,] 90 135 38 27 12 15 0.5555556 [53,] 64 136 110 75 44 31 0.4133333 [54,] 65 136 75 51 30 21 0.4117647 [55,] 108 136 57 37 14 23 0.6216216 [56,] 133 136 70 40 26 14 0.3500000 [57,] 53 137 69 44 24 19 0.4318182 [58,] 54 137 113 73 44 29 0.3972603 [59,] 55 137 112 64 41 23 0.3593750 [60,] 56 137 58 37 23 14 0.3783784 [61,] 57 137 63 42 27 15 0.3571429 [62,] 58 137 92 51 29 22 0.4313725 [63,] 258 137 64 42 27 15 0.3571429 [64,] 5 138 80 47 25 22 0.4680851 [65,] 56 138 82 45 31 14 0.3111111 [66,] 57 138 95 60 40 20 0.3333333 [67,] 58 138 69 47 32 15 0.3191489 [68,] 46 145 44 30 19 11 0.3666667 [69,] 91 145 69 48 15 32 0.6666667 [70,] 92 145 58 41 19 22 0.5365854 [71,] 316 145 72 51 28 22 0.4313725 [72,] 3 146 68 49 27 22 0.4489796 [73,] 39 146 53 34 20 14 0.4117647 [74,] 76 146 73 48 29 19 0.3958333 [75,] 105 146 39 21 7 14 0.6666667 [76,] 285 146 65 43 20 22 0.5116279 [77,] 81 154 46 35 12 22 0.6285714 [78,] 5 155 44 34 12 21 0.6176471 [79,] 99 156 72 26 16 10 0.3846154 [80,] 5 157 87 34 23 11 0.3235294 [81,] 25 164 31 17 7 10 0.5882353 [82,] 47 165 51 33 12 21 0.6363636 [83,] 12 166 123 80 55 25 0.3125000 [84,] 12 170 116 69 39 30 0.4347826 [85,] 13 170 63 42 26 16 0.3809524 [86,] 60 170 106 60 32 27 0.4500000 [87,] 13 171 108 61 33 27 0.4426230 [88,] 14 171 50 28 18 10 0.3571429 [89,] 108 171 76 44 16 28 0.6363636 [90,] 178 171 38 27 16 11 0.4074074 [91,] 100 172 96 70 46 24 0.3428571 [92,] 272 172 44 32 20 12 0.3750000 [93,] 61 174 39 28 13 14 0.5000000 [94,] 11 224 46 21 12 9 0.4285714 [95,] 13 224 52 23 15 8 0.3478261 [96,] 43 224 58 35 18 16 0.4571429 [97,] 230 224 62 37 19 17 0.4594595 [98,] 6 225 36 17 8 9 0.5294118 [99,] 7 225 39 17 9 8 0.4705882 [100,] 17 225 51 39 20 19 0.4871795 [101,] 57 226 43 32 14 17 0.5312500 [102,] 59 227 43 27 14 13 0.4814815 [103,] 18 229 100 54 32 22 0.4074074 [104,] 56 229 118 75 40 35 0.4666667 [105,] 269 229 93 58 28 30 0.5172414 [106,] 9 230 125 80 46 34 0.4250000 [107,] 16 231 91 64 31 33 0.5156250 [108,] 248 231 69 45 20 25 0.5555556 [109,] 3 232 101 70 35 35 0.5000000 [110,] 69 232 56 39 19 20 0.5128205 [111,] 34 234 42 24 10 14 0.5833333 [112,] 5 244 66 45 29 15 0.3333333 [113,] 172 244 66 48 32 15 0.3125000 [114,] 23 245 75 56 37 18 0.3214286 [115,] 233 268 39 26 16 9 0.3461538 [116,] 96 269 35 23 13 9 0.3913043 [117,] 59 309 31 21 10 11 0.5238095 [118,] 9 335 35 24 7 17 0.7083333 [119,] 47 335 37 24 6 18 0.7500000 [120,] 114 335 53 38 5 33 0.8684211 [121,] 98 348 62 43 29 14 0.3255814 [122,] 25 356 63 45 31 14 0.3111111 [123,] 64 356 43 32 18 14 0.4375000 [124,] 201 356 58 42 19 23 0.5476190 [125,] 202 356 61 46 20 26 0.5652174 [126,] 1 357 59 44 28 16 0.3636364 [127,] 2 357 40 31 19 12 0.3870968 [128,] 3 357 82 63 25 38 0.6031746 [129,] 10 357 59 42 18 24 0.5714286 [130,] 39 358 58 41 17 24 0.5853659 [131,] 43 358 62 40 25 15 0.3750000 [132,] 1 359 44 27 18 9 0.3333333 [133,] 52 375 39 24 15 9 0.3750000 [134,] 54 375 43 23 14 9 0.3913043 [135,] 4 376 44 24 15 9 0.3750000 [136,] 35 376 42 27 9 18 0.6666667 [137,] 4 377 109 72 30 41 0.5694444 [138,] 5 377 103 75 24 51 0.6800000 [139,] 6 377 80 53 32 20 0.3773585 [140,] 7 377 62 40 25 14 0.3500000 [141,] 22 378 63 50 27 22 0.4400000 [142,] 29 378 116 77 35 41 0.5324675 [143,] 31 378 108 78 27 51 0.6538462 [144,] 32 378 93 63 42 20 0.3174603 [145,] 33 378 69 44 28 15 0.3409091 [146,] 41 378 57 38 9 29 0.7631579 [147,] 42 378 38 25 12 12 0.4800000 [148,] 193 378 53 33 16 17 0.5151515 [149,] 1 379 59 41 28 13 0.3170732 [150,] 8 379 70 50 13 37 0.7400000 [151,] 73 379 46 31 17 13 0.4193548 [152,] 40 383 108 74 50 24 0.3243243 [153,] 96 383 64 37 12 25 0.6756757 [154,] 8 384 52 35 23 12 0.3428571 [155,] 47 384 115 78 54 24 0.3076923 [156,] 57 384 42 27 8 19 0.7037037 [157,] 58 384 57 40 16 24 0.6000000 [158,] 66 384 115 69 35 34 0.4927536 [159,] 67 384 93 61 36 24 0.3934426 [160,] 105 384 78 54 19 35 0.6481481 [161,] 263 384 34 19 10 9 0.4736842 [162,] 3 385 55 35 16 19 0.5428571 [163,] 34 385 68 41 23 18 0.4390244 [164,] 35 385 84 55 30 24 0.4363636 [165,] 100 385 60 43 19 24 0.5581395 [166,] 223 385 42 30 17 13 0.4333333 [167,] 57 390 61 46 23 23 0.5000000 [168,] 68 390 56 40 14 26 0.6500000 [169,] 17 391 64 47 21 26 0.5531915 [170,] 31 391 81 55 28 27 0.4909091 [171,] 58 391 85 60 32 28 0.4666667 [172,] 172 391 38 27 13 14 0.5185185 [173,] 31 392 67 45 18 27 0.6000000 [174,] 113 392 77 53 26 27 0.5094340 [175,] 41 396 53 33 13 19 0.5757576 [176,] 27 397 45 28 13 14 0.5000000 [177,] 40 422 84 58 33 24 0.4137931 [178,] 56 422 34 20 4 16 0.8000000 [179,] 233 422 43 31 11 20 0.6451613 [180,] 145 423 52 36 9 26 0.7222222 [181,] 33 449 56 36 20 16 0.4444444 [182,] 34 449 34 22 12 9 0.4090909 [183,] 36 449 62 41 24 17 0.4146341 [184,] 3 450 56 38 22 16 0.4210526 [185,] 120 451 66 47 24 23 0.4893617 [186,] 3 452 77 54 31 23 0.4259259 [187,] 4 470 90 46 13 32 0.6956522 [188,] 5 470 100 54 23 31 0.5740741 [189,] 146 470 80 41 22 19 0.4634146 [190,] 14 471 94 48 15 32 0.6666667 [191,] 165 471 90 48 28 20 0.4166667 [192,] 152 475 49 22 12 10 0.4545455 [193,] 29 486 80 56 32 22 0.3928571 [194,] 41 486 47 31 13 18 0.5806452 [195,] 42 486 99 57 32 25 0.4385965 [196,] 43 486 81 58 35 22 0.3793103 [197,] 44 486 62 28 15 12 0.4285714 [198,] 45 486 83 39 17 22 0.5641026 [199,] 49 486 114 77 49 26 0.3376623 [200,] 50 486 78 47 24 22 0.4680851 [201,] 2 487 112 62 37 25 0.4032258 [202,] 4 487 64 46 27 18 0.3913043 [203,] 9 487 116 57 35 21 0.3684211 [204,] 12 487 91 61 36 22 0.3606557 [205,] 28 487 60 34 16 18 0.5294118 [206,] 35 487 62 43 29 14 0.3255814 [207,] 39 487 44 22 11 11 0.5000000 [208,] 85 487 31 15 9 6 0.4000000 [209,] 183 487 49 36 23 12 0.3333333 [210,] 192 487 59 36 19 16 0.4444444 [211,] 197 487 43 29 17 12 0.4137931 [212,] 200 487 39 23 16 7 0.3043478 [213,] 48 488 44 29 18 10 0.3448276 [214,] 49 488 69 47 30 17 0.3617021 [215,] 51 488 62 34 22 12 0.3529412 [216,] 52 488 68 41 28 13 0.3170732 [217,] 247 488 35 19 11 8 0.4210526 [218,] 261 489 36 20 12 8 0.4000000 [219,] 60 503 77 49 30 17 0.3469388 [220,] 61 503 77 51 34 16 0.3137255 [221,] 84 512 52 42 19 23 0.5476190 [222,] 95 519 45 27 13 14 0.5185185 [223,] 35 521 48 30 20 10 0.3333333 [224,] 10 534 36 23 16 7 0.3043478 [225,] 31 538 78 52 29 23 0.4423077 [226,] 62 538 105 66 37 29 0.4393939 [227,] 63 538 48 34 15 18 0.5294118 [228,] 66 538 70 40 20 19 0.4750000 [229,] 68 538 91 55 24 30 0.5454545 [230,] 158 538 100 53 25 28 0.5283019 [231,] 159 538 37 22 12 10 0.4545455 [232,] 170 538 55 31 18 12 0.3870968 [233,] 5 539 91 61 37 23 0.3770492 [234,] 7 539 38 23 4 19 0.8260870 [235,] 9 539 89 53 13 40 0.7547170 [236,] 10 539 65 44 23 21 0.4772727 [237,] 15 539 116 63 31 31 0.4920635 [238,] 72 539 46 32 21 11 0.3437500 [239,] 94 539 67 49 25 23 0.4693878 [240,] 65 540 107 61 29 31 0.5081967 [241,] 132 540 100 55 28 26 0.4727273 [242,] 46 550 87 63 44 19 0.3015873 [243,] 72 551 56 40 27 13 0.3250000 [244,] 15 554 254 144 54 90 0.6250000 [245,] 39 554 182 98 37 61 0.6224490 [246,] 40 554 58 35 13 22 0.6285714 [247,] 66 554 102 69 25 44 0.6376812 [248,] 74 554 59 44 16 27 0.6136364 [249,] 98 554 127 65 33 32 0.4923077 [250,] 114 554 96 64 18 46 0.7187500 [251,] 130 554 110 69 30 39 0.5652174 [252,] 242 554 111 73 25 47 0.6438356 [253,] 260 554 161 91 43 48 0.5274725 [254,] 7 555 118 77 30 47 0.6103896 [255,] 58 555 50 39 26 12 0.3076923 [256,] 76 555 41 35 7 27 0.7714286 [257,] 122 555 100 58 31 27 0.4655172 [258,] 241 555 101 68 21 46 0.6764706 [259,] 39 556 104 73 24 49 0.6712329 [260,] 26 557 99 67 20 47 0.7014925 [261,] 27 557 86 63 15 48 0.7619048 [262,] 48 561 46 33 13 19 0.5757576 [263,] 50 561 45 26 17 9 0.3461538 [264,] 53 561 78 49 21 28 0.5714286 [265,] 82 561 49 39 16 22 0.5641026 [266,] 133 561 91 57 27 30 0.5263158 [267,] 34 562 36 29 7 21 0.7241379 [268,] 36 562 42 25 16 9 0.3600000 [269,] 37 562 92 57 26 31 0.5438596 [270,] 38 562 72 46 21 25 0.5434783 [271,] 75 562 74 59 39 19 0.3220339 [272,] 69 563 52 34 22 12 0.3529412 [273,] 70 563 110 68 38 30 0.4411765 [274,] 3 564 71 46 25 21 0.4565217 [275,] 85 564 45 30 18 12 0.4000000 [276,] 152 564 94 57 31 26 0.4561404 [277,] 4 565 31 25 15 10 0.4000000 [278,] 7 565 37 27 12 14 0.5185185 [279,] 72 565 68 47 29 17 0.3617021 [280,] 81 565 50 40 27 13 0.3250000 [281,] 87 565 63 49 25 23 0.4693878 [282,] 16 566 69 48 30 17 0.3541667 [283,] 57 566 36 26 12 13 0.5000000 [284,] 7 570 63 50 24 24 0.4800000 [285,] 35 571 77 54 31 22 0.4074074 [286,] 38 571 49 36 17 17 0.4722222 [287,] 48 571 80 60 18 42 0.7000000 [288,] 65 571 37 28 12 15 0.5357143 [289,] 7 572 72 52 28 22 0.4230769 [290,] 22 572 77 49 32 16 0.3265306 [291,] 16 573 91 60 41 19 0.3166667 [292,] 70 573 66 52 29 23 0.4423077 [293,] 240 573 41 33 18 15 0.4545455 [294,] 35 574 88 58 39 19 0.3275862 [295,] 36 574 62 49 25 24 0.4897959 [296,] 242 574 41 29 19 10 0.3448276 [297,] 28 585 60 39 21 18 0.4615385 [298,] 43 585 53 37 25 12 0.3243243 [299,] 22 589 104 68 39 28 0.4117647 [300,] 37 589 72 42 20 22 0.5238095 [301,] 9 590 79 48 24 23 0.4791667 [302,] 55 590 71 42 19 23 0.5476190 [303,] 66 590 80 53 29 23 0.4339623 [304,] 191 590 64 38 16 22 0.5789474 [305,] 65 610 50 26 18 8 0.3076923 [306,] 216 610 39 21 12 9 0.4285714 [307,] 37 615 54 37 24 13 0.3513514 [308,] 19 616 37 23 15 8 0.3478261 [309,] 204 616 34 23 15 8 0.3478261 [310,] 88 627 63 43 21 21 0.4883721 [311,] 12 628 79 57 35 21 0.3684211 > #ancientS1: posAll <- 470 ibdC <- 4 #ancientS2: posAll <- 229 ibdC <- 56 #ancientS3: posAll <- 123 ibdC <- 47 #neanderS1: posAll <- 384 ibdC <- 57 #neanderS1: posAll <- 554 ibdC <- 39 #ancientS4: posAll <- 377 ibdC <- 5 posAll <- 377 ibdC <- 5 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="ancientS4" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ae <- which(AncestMat[,12]>0.3) AFR1 <- which(PopulationMat[,6]>0.2) ASN1 <- which(PopulationMat[,8]>0.2) aeASN <- intersect(ASN1,ae) aeANSAFR <- intersect(aeASN,AFR1) au <- which(AncestMat[,5]>30) auANSAFR <- intersect(au,aeANSAFR) AncestMat[auANSAFR,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 82 20 49 45 31 14 0.3111111 [2,] 96 28 37 36 22 14 0.3888889 [3,] 256 28 36 35 23 12 0.3428571 [4,] 10 29 86 86 58 27 0.3139535 [5,] 74 29 42 41 25 16 0.3902439 [6,] 10 38 39 13 7 6 0.4615385 [7,] 36 39 37 13 7 6 0.4615385 [8,] 191 39 100 100 65 35 0.3500000 [9,] 46 41 77 77 53 24 0.3116883 [10,] 94 43 100 98 62 36 0.3673469 [11,] 61 45 57 57 39 18 0.3157895 [12,] 9 55 39 39 24 12 0.3076923 [13,] 61 85 33 6 3 3 0.5000000 [14,] 40 91 61 61 41 20 0.3278689 [15,] 260 102 70 70 47 22 0.3142857 [16,] 74 122 39 39 23 16 0.4102564 [17,] 17 130 59 59 38 20 0.3389831 [18,] 142 130 40 40 23 16 0.4000000 [19,] 39 131 116 112 77 34 0.3035714 [20,] 57 131 131 130 83 47 0.3615385 [21,] 60 131 157 153 106 47 0.3071895 [22,] 61 131 139 136 90 46 0.3382353 [23,] 62 131 150 138 79 59 0.4275362 [24,] 1 132 42 42 27 15 0.3571429 [25,] 44 132 73 70 41 29 0.4142857 [26,] 46 132 149 137 79 58 0.4233577 [27,] 55 132 94 90 55 35 0.3888889 [28,] 215 132 114 113 67 46 0.4070796 [29,] 237 132 101 101 67 34 0.3366337 [30,] 90 135 38 37 19 17 0.4594595 [31,] 108 136 57 56 31 24 0.4285714 [32,] 55 137 112 112 74 37 0.3303571 [33,] 56 138 82 82 55 26 0.3170732 [34,] 46 145 44 43 29 14 0.3255814 [35,] 39 146 53 52 35 17 0.3269231 [36,] 81 154 46 46 32 14 0.3043478 [37,] 5 155 44 44 30 14 0.3181818 [38,] 14 171 50 50 30 19 0.3800000 [39,] 108 171 76 76 46 30 0.3947368 [40,] 178 171 38 38 24 13 0.3421053 [41,] 61 174 39 38 21 17 0.4473684 [42,] 18 227 42 42 27 15 0.3571429 [43,] 185 227 79 79 48 29 0.3670886 [44,] 86 228 83 83 53 29 0.3493976 [45,] 98 228 40 40 25 15 0.3750000 [46,] 18 229 100 100 63 36 0.3600000 [47,] 40 229 172 172 114 58 0.3372093 [48,] 269 229 93 93 59 33 0.3548387 [49,] 4 230 170 170 112 57 0.3352941 [50,] 61 230 108 108 75 33 0.3055556 [51,] 248 231 69 69 47 22 0.3188406 [52,] 3 232 101 101 70 31 0.3069307 [53,] 69 232 56 56 33 23 0.4107143 [54,] 43 251 48 48 32 15 0.3125000 [55,] 214 266 65 64 44 20 0.3125000 [56,] 233 268 39 39 23 15 0.3846154 [57,] 96 269 35 35 20 14 0.4000000 [58,] 21 287 84 84 46 38 0.4523810 [59,] 184 287 90 84 48 33 0.3928571 [60,] 16 288 98 93 51 41 0.4408602 [61,] 11 290 96 96 65 30 0.3125000 [62,] 246 290 43 43 26 16 0.3720930 [63,] 8 291 93 93 62 30 0.3225806 [64,] 37 291 55 55 36 18 0.3272727 [65,] 85 292 60 59 32 27 0.4576271 [66,] 59 309 31 31 9 21 0.6774194 [67,] 9 335 35 35 16 19 0.5428571 [68,] 47 335 37 37 20 17 0.4594595 [69,] 114 335 53 53 27 26 0.4905660 [70,] 146 342 42 26 11 15 0.5769231 [71,] 177 348 46 7 3 4 0.5714286 [72,] 286 354 64 53 36 17 0.3207547 [73,] 52 375 39 38 26 12 0.3157895 [74,] 4 377 109 109 73 36 0.3302752 [75,] 5 377 103 103 70 32 0.3106796 [76,] 29 378 116 116 79 37 0.3189655 [77,] 41 378 57 57 39 18 0.3157895 [78,] 42 378 38 38 23 15 0.3947368 [79,] 193 378 53 53 37 16 0.3018868 [80,] 8 379 70 70 47 23 0.3285714 [81,] 73 379 46 44 27 17 0.3863636 [82,] 96 383 64 64 40 24 0.3750000 [83,] 66 384 115 114 79 35 0.3070175 [84,] 67 384 93 92 63 29 0.3152174 [85,] 5 385 95 92 60 31 0.3369565 [86,] 35 385 84 84 55 29 0.3452381 [87,] 75 389 109 108 71 37 0.3425926 [88,] 62 390 107 106 70 36 0.3396226 [89,] 31 392 67 67 46 21 0.3134328 [90,] 120 451 66 66 46 20 0.3030303 [91,] 4 470 90 82 51 31 0.3780488 [92,] 14 471 94 85 54 31 0.3647059 [93,] 152 475 49 49 30 18 0.3673469 [94,] 29 486 80 80 52 28 0.3500000 [95,] 41 486 47 25 17 8 0.3200000 [96,] 50 486 78 78 52 26 0.3333333 [97,] 12 487 91 91 62 29 0.3186813 [98,] 85 487 31 31 19 12 0.3870968 [99,] 192 487 59 59 37 22 0.3728814 [100,] 200 487 39 39 27 12 0.3076923 [101,] 48 488 44 44 27 17 0.3863636 [102,] 60 503 77 77 51 25 0.3246753 [103,] 35 519 67 67 45 21 0.3134328 [104,] 1 520 67 67 45 21 0.3134328 [105,] 35 521 48 48 30 18 0.3750000 [106,] 39 522 111 111 74 37 0.3333333 [107,] 10 534 36 35 19 16 0.4571429 [108,] 13 538 128 127 75 51 0.4015748 [109,] 29 538 147 146 87 58 0.3972603 [110,] 31 538 78 77 45 31 0.4025974 [111,] 62 538 105 104 68 36 0.3461538 [112,] 63 538 48 48 27 21 0.4375000 [113,] 68 538 91 90 56 33 0.3666667 [114,] 159 538 37 37 15 21 0.5675676 [115,] 4 539 213 212 144 67 0.3160377 [116,] 5 539 91 91 63 28 0.3076923 [117,] 7 539 38 38 22 16 0.4210526 [118,] 9 539 89 88 46 41 0.4659091 [119,] 10 539 65 65 37 27 0.4153846 [120,] 15 539 116 113 76 37 0.3274336 [121,] 72 539 46 45 24 20 0.4444444 [122,] 94 539 67 67 41 26 0.3880597 [123,] 213 539 102 101 52 48 0.4752475 [124,] 65 540 107 103 66 37 0.3592233 [125,] 132 540 100 97 61 36 0.3711340 [126,] 54 551 49 49 31 18 0.3673469 [127,] 72 551 56 56 36 19 0.3392857 [128,] 15 554 254 254 173 79 0.3110236 [129,] 39 554 182 182 125 55 0.3021978 [130,] 40 554 58 58 34 23 0.3965517 [131,] 66 554 102 102 66 36 0.3529412 [132,] 114 554 96 96 64 31 0.3229167 [133,] 130 554 110 110 73 36 0.3272727 [134,] 260 554 161 161 107 52 0.3229814 [135,] 7 555 118 118 79 38 0.3220339 [136,] 27 557 86 86 60 26 0.3023256 [137,] 133 561 91 90 56 33 0.3666667 [138,] 37 562 92 91 56 33 0.3626374 [139,] 81 565 50 50 31 18 0.3600000 [140,] 87 565 63 63 39 23 0.3650794 [141,] 48 571 80 80 52 28 0.3500000 [142,] 66 590 80 79 49 28 0.3544304 [143,] 216 610 39 39 26 13 0.3333333 [144,] 37 615 54 54 32 22 0.4074074 [145,] 83 615 72 72 46 26 0.3611111 [146,] 19 616 37 37 24 12 0.3243243 [147,] 204 616 34 34 21 13 0.3823529 [148,] 129 619 56 56 39 17 0.3035714 [149,] 141 619 50 50 28 22 0.4400000 [150,] 88 627 63 63 43 19 0.3015873 [151,] 12 628 79 79 54 24 0.3037975 [152,] 48 628 38 38 24 13 0.3421053 #ancestS1: posAll <- 292 ibdC <- 85 #ancestS2: posAll <- 287 ibdC <- 21 #ancestS3: posAll <- 229 ibdC <- 40 #ancestS4: posAll <- 132 ibdC <- 215 posAll <- 132 ibdC <- 215 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="ancestS4" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ae <- which(AncestMat[,12]>0.5) au <- which(AncestMat[,5]>30) as <- intersect(ae,au) AncestMat[as,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 223 1 42 1 0 1 1.0000000 [2,] 8 20 53 45 21 24 0.5333333 [3,] 116 48 43 9 3 6 0.6666667 [4,] 118 48 35 4 1 3 0.7500000 [5,] 19 49 45 11 4 7 0.6363636 [6,] 114 64 33 24 8 16 0.6666667 [7,] 115 64 39 28 7 20 0.7142857 [8,] 132 72 39 35 16 19 0.5428571 [9,] 171 74 59 42 19 23 0.5476190 [10,] 19 87 31 30 14 16 0.5333333 [11,] 17 93 57 57 16 41 0.7192982 [12,] 196 93 31 31 12 18 0.5806452 [13,] 65 94 65 61 25 36 0.5901639 [14,] 66 94 52 52 16 35 0.6730769 [15,] 84 101 32 31 13 17 0.5483871 [16,] 47 106 34 34 13 20 0.5882353 [17,] 67 148 36 36 13 23 0.6388889 [18,] 230 148 41 41 17 24 0.5853659 [19,] 140 149 49 49 22 27 0.5510204 [20,] 87 159 36 35 9 25 0.7142857 [21,] 116 177 35 35 13 22 0.6285714 [22,] 66 178 44 44 20 24 0.5454545 [23,] 35 186 35 35 13 21 0.6000000 [24,] 74 186 38 36 9 27 0.7500000 [25,] 7 187 37 37 15 21 0.5675676 [26,] 55 187 31 29 13 16 0.5517241 [27,] 1 196 39 39 14 24 0.6153846 [28,] 112 196 34 34 10 24 0.7058824 [29,] 44 204 37 37 10 26 0.7027027 [30,] 36 210 87 85 42 43 0.5058824 [31,] 2 211 86 84 41 43 0.5119048 [32,] 20 211 56 56 27 29 0.5178571 [33,] 198 226 80 80 39 41 0.5125000 [34,] 13 227 53 48 22 26 0.5416667 [35,] 78 254 45 45 14 31 0.6888889 [36,] 78 255 46 46 15 31 0.6739130 [37,] 26 258 59 58 21 36 0.6206897 [38,] 30 259 58 57 20 36 0.6315789 [39,] 32 259 54 53 17 36 0.6792453 [40,] 63 259 54 47 22 25 0.5319149 [41,] 64 259 32 25 8 17 0.6800000 [42,] 66 259 51 51 12 39 0.7647059 [43,] 67 259 52 52 11 41 0.7884615 [44,] 149 259 40 39 16 23 0.5897436 [45,] 6 260 46 46 20 26 0.5652174 [46,] 7 260 55 48 17 31 0.6458333 [47,] 41 260 38 37 13 24 0.6486486 [48,] 127 263 60 57 22 35 0.6140351 [49,] 37 264 44 41 19 22 0.5365854 [50,] 72 264 56 52 21 31 0.5961538 [51,] 148 272 32 31 15 16 0.5161290 [52,] 108 273 35 33 16 17 0.5151515 [53,] 51 274 49 49 23 26 0.5306122 [54,] 83 275 38 38 18 20 0.5263158 [55,] 184 275 36 36 14 22 0.6111111 [56,] 152 291 40 40 15 24 0.6000000 [57,] 54 293 39 38 6 32 0.8421053 [58,] 78 294 38 38 6 32 0.8421053 [59,] 220 295 60 60 21 38 0.6333333 [60,] 110 296 74 74 33 39 0.5270270 [61,] 41 304 41 41 20 21 0.5121951 [62,] 11 306 51 51 18 33 0.6470588 [63,] 210 306 32 32 15 17 0.5312500 [64,] 11 307 47 47 17 30 0.6382979 [65,] 64 307 74 73 33 37 0.5068493 [66,] 59 309 31 31 9 21 0.6774194 [67,] 39 333 35 28 12 16 0.5714286 [68,] 14 334 35 33 8 24 0.7272727 [69,] 9 335 35 35 16 19 0.5428571 [70,] 31 337 50 50 22 28 0.5600000 [71,] 146 342 42 26 11 15 0.5769231 [72,] 33 343 42 38 15 22 0.5789474 [73,] 55 343 31 17 5 12 0.7058824 [74,] 175 343 32 17 8 9 0.5294118 [75,] 12 344 55 23 9 14 0.6086957 [76,] 2 345 37 11 2 9 0.8181818 [77,] 52 345 35 13 3 10 0.7692308 [78,] 54 345 31 9 2 7 0.7777778 [79,] 59 345 31 31 11 20 0.6451613 [80,] 271 345 31 14 5 9 0.6428571 [81,] 15 346 34 34 13 21 0.6176471 [82,] 177 348 46 7 3 4 0.5714286 [83,] 55 354 51 51 23 28 0.5490196 [84,] 55 355 34 34 15 19 0.5588235 [85,] 131 355 35 35 16 19 0.5428571 [86,] 24 373 51 38 17 21 0.5526316 [87,] 103 373 60 60 28 32 0.5333333 [88,] 137 373 43 43 16 26 0.6046512 [89,] 19 382 33 33 13 20 0.6060606 [90,] 9 383 36 36 16 20 0.5555556 [91,] 10 384 34 34 13 21 0.6176471 [92,] 6 385 41 41 18 23 0.5609756 [93,] 63 406 52 52 22 30 0.5769231 [94,] 221 406 60 60 27 33 0.5500000 [95,] 79 421 124 124 55 67 0.5403226 [96,] 94 423 61 61 26 35 0.5737705 [97,] 97 423 74 73 36 37 0.5068493 [98,] 266 423 68 68 26 42 0.6176471 [99,] 73 424 49 49 22 27 0.5510204 [100,] 223 424 68 68 26 42 0.6176471 [101,] 22 434 40 40 19 21 0.5250000 [102,] 125 434 47 47 22 25 0.5319149 [103,] 115 435 39 39 16 23 0.5897436 [104,] 109 436 46 44 21 23 0.5227273 [105,] 74 438 39 38 18 20 0.5263158 [106,] 34 454 41 41 15 25 0.6097561 [107,] 29 455 39 39 14 24 0.6153846 [108,] 93 455 78 77 29 48 0.6233766 [109,] 251 455 33 33 8 25 0.7575758 [110,] 212 457 32 32 13 18 0.5625000 [111,] 6 458 40 40 16 23 0.5750000 [112,] 57 460 38 38 13 24 0.6315789 [113,] 9 461 37 37 12 24 0.6486486 [114,] 298 461 148 148 71 75 0.5067568 [115,] 52 469 42 42 16 26 0.6190476 [116,] 101 469 47 47 16 31 0.6595745 [117,] 108 477 62 60 27 31 0.5166667 [118,] 136 477 46 44 14 30 0.6818182 [119,] 29 478 57 55 25 29 0.5272727 [120,] 95 478 49 47 19 28 0.5957447 [121,] 85 484 38 34 16 18 0.5294118 [122,] 86 484 35 35 15 19 0.5428571 [123,] 32 513 33 33 14 19 0.5757576 [124,] 23 526 33 33 16 17 0.5151515 [125,] 153 528 36 34 10 23 0.6764706 [126,] 159 528 36 36 15 21 0.5833333 [127,] 34 529 40 40 19 21 0.5250000 [128,] 159 538 37 37 15 21 0.5675676 [129,] 28 549 32 32 11 21 0.6562500 [130,] 5 550 40 40 18 21 0.5250000 [131,] 1 551 32 32 14 17 0.5312500 [132,] 25 553 45 45 22 23 0.5111111 [133,] 15 560 39 39 13 26 0.6666667 [134,] 26 562 38 38 17 20 0.5263158 [135,] 41 563 32 32 14 17 0.5312500 [136,] 62 580 46 45 20 25 0.5555556 [137,] 85 616 46 46 21 25 0.5434783 [138,] 99 619 40 38 17 20 0.5263158 [139,] 106 622 31 31 14 17 0.5483871 [140,] 59 625 49 49 18 31 0.6326531 [141,] 90 629 80 80 32 48 0.6000000 [142,] 181 639 31 5 2 3 0.6000000 > name="ancestT1" posAll <- 294 ibdC <- 78 name="ancestT2" posAll <- 186 ibdC <- 74 posAll <- 186 ibdC <- 74 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="ancestT2" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ae <- which(DenisovaMat[,12]>0.6) au <- which(DenisovaMat[,5]>40) as <- intersect(ae,au) DenisovaMat[as,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 1 1 57 57 17 39 0.6842105 [2,] 6 3 72 72 23 49 0.6805556 [3,] 3 4 48 48 13 35 0.7291667 [4,] 56 15 76 76 29 47 0.6184211 [5,] 12 28 85 85 26 59 0.6941176 [6,] 203 28 71 71 24 47 0.6619718 [7,] 2 30 73 73 29 44 0.6027397 [8,] 3 30 80 80 26 53 0.6625000 [9,] 4 30 64 64 19 43 0.6718750 [10,] 5 35 46 46 17 28 0.6086957 [11,] 98 36 46 46 18 28 0.6086957 [12,] 191 39 100 100 36 64 0.6400000 [13,] 61 45 57 57 20 37 0.6491228 [14,] 58 51 46 46 15 31 0.6739130 [15,] 20 57 43 43 12 31 0.7209302 [16,] 37 66 50 50 13 37 0.7400000 [17,] 132 71 160 160 63 97 0.6062500 [18,] 92 86 81 81 22 59 0.7283951 [19,] 93 86 68 68 24 44 0.6470588 [20,] 47 87 71 71 16 55 0.7746479 [21,] 48 87 67 67 23 44 0.6567164 [22,] 68 87 46 46 15 30 0.6521739 [23,] 42 89 75 75 23 51 0.6800000 [24,] 59 89 49 49 17 32 0.6530612 [25,] 17 93 57 57 18 39 0.6842105 [26,] 62 96 42 42 7 35 0.8333333 [27,] 106 96 43 43 13 30 0.6976744 [28,] 166 101 62 62 21 41 0.6612903 [29,] 5 103 116 116 44 72 0.6206897 [30,] 114 106 55 55 20 35 0.6363636 [31,] 145 123 43 43 14 27 0.6279070 [32,] 102 128 74 74 25 49 0.6621622 [33,] 103 128 63 63 21 42 0.6666667 [34,] 2 129 64 64 24 40 0.6250000 [35,] 3 129 55 55 19 36 0.6545455 [36,] 4 129 71 71 28 43 0.6056338 [37,] 5 129 59 59 13 46 0.7796610 [38,] 157 129 77 77 26 51 0.6623377 [39,] 1 130 44 44 9 35 0.7954545 [40,] 16 130 54 54 17 36 0.6666667 [41,] 17 130 59 59 20 38 0.6440678 [42,] 57 131 131 131 41 90 0.6870229 [43,] 61 131 139 139 49 90 0.6474820 [44,] 62 131 150 150 46 102 0.6800000 [45,] 77 131 55 55 18 36 0.6545455 [46,] 78 131 125 125 26 99 0.7920000 [47,] 80 131 78 78 20 57 0.7307692 [48,] 116 131 52 52 17 35 0.6730769 [49,] 2 132 149 149 34 114 0.7651007 [50,] 44 132 73 73 13 60 0.8219178 [51,] 46 132 149 149 45 102 0.6845638 [52,] 215 132 114 114 30 84 0.7368421 [53,] 111 134 70 70 15 55 0.7857143 [54,] 110 143 68 68 22 45 0.6617647 [55,] 111 143 41 41 14 27 0.6585366 [56,] 51 161 45 45 9 36 0.8000000 [57,] 52 161 49 49 15 34 0.6938776 [58,] 32 167 70 70 11 58 0.8285714 [59,] 108 171 76 76 24 52 0.6842105 [60,] 102 172 82 82 21 60 0.7317073 [61,] 16 176 59 59 19 40 0.6779661 [62,] 3 177 50 50 10 40 0.8000000 [63,] 76 201 70 70 26 44 0.6285714 [64,] 77 201 89 89 31 57 0.6404494 [65,] 12 202 66 66 19 47 0.7121212 [66,] 90 202 45 45 15 29 0.6444444 [67,] 195 202 56 56 15 41 0.7321429 [68,] 3 203 72 72 25 47 0.6527778 [69,] 171 203 63 63 22 41 0.6507937 [70,] 227 223 61 61 19 42 0.6885246 [71,] 50 224 56 56 20 36 0.6428571 [72,] 17 225 51 51 18 31 0.6078431 [73,] 57 226 43 43 14 28 0.6511628 [74,] 80 227 44 44 17 27 0.6136364 [75,] 269 229 93 93 32 60 0.6451613 [76,] 25 236 42 42 14 28 0.6666667 [77,] 32 259 54 54 17 37 0.6851852 [78,] 63 259 54 54 13 41 0.7592593 [79,] 66 259 51 51 10 41 0.8039216 [80,] 67 259 52 52 6 46 0.8846154 [81,] 6 260 46 46 13 33 0.7173913 [82,] 7 260 55 55 12 43 0.7818182 [83,] 47 260 41 41 13 26 0.6341463 [84,] 127 263 60 60 17 43 0.7166667 [85,] 37 264 44 44 16 28 0.6363636 [86,] 72 264 56 56 18 38 0.6785714 [87,] 35 277 56 56 21 35 0.6250000 [88,] 6 278 55 55 20 35 0.6363636 [89,] 33 293 88 88 18 70 0.7954545 [90,] 70 293 76 76 23 53 0.6973684 [91,] 11 294 79 79 25 54 0.6835443 [92,] 12 294 84 84 15 69 0.8214286 [93,] 220 295 60 60 21 39 0.6500000 [94,] 48 299 48 48 19 29 0.6041667 [95,] 55 305 92 92 33 59 0.6413043 [96,] 254 305 46 46 12 34 0.7391304 [97,] 11 306 51 51 17 34 0.6666667 [98,] 32 306 95 95 36 59 0.6210526 [99,] 11 307 47 47 15 32 0.6808511 [100,] 15 329 93 93 33 60 0.6451613 [101,] 57 330 90 90 29 61 0.6777778 [102,] 62 334 57 57 17 40 0.7017544 [103,] 114 335 53 53 5 48 0.9056604 [104,] 78 338 43 43 14 29 0.6744186 [105,] 72 339 43 43 14 29 0.6744186 [106,] 88 340 55 55 16 39 0.7090909 [107,] 89 340 53 53 17 35 0.6603774 [108,] 5 347 90 90 31 59 0.6555556 [109,] 201 356 58 58 21 37 0.6379310 [110,] 202 356 61 61 15 46 0.7540984 [111,] 3 357 82 82 23 58 0.7073171 [112,] 257 357 75 75 28 47 0.6266667 [113,] 9 358 82 82 30 52 0.6341463 [114,] 265 358 68 68 26 42 0.6176471 [115,] 67 367 73 73 21 52 0.7123288 [116,] 51 368 54 54 16 38 0.7037037 [117,] 91 368 72 72 20 52 0.7222222 [118,] 14 372 55 55 16 38 0.6909091 [119,] 18 372 59 59 16 43 0.7288136 [120,] 249 372 76 76 29 46 0.6052632 [121,] 261 372 89 89 33 54 0.6067416 [122,] 103 373 60 60 15 45 0.7500000 [123,] 252 383 45 45 14 30 0.6666667 [124,] 19 384 50 50 18 31 0.6200000 [125,] 80 384 54 54 20 33 0.6111111 [126,] 6 385 41 41 11 30 0.7317073 [127,] 8 389 112 112 33 78 0.6964286 [128,] 9 389 129 129 25 103 0.7984496 [129,] 59 406 66 66 26 40 0.6060606 [130,] 8 407 50 50 15 35 0.7000000 [131,] 9 407 61 61 16 45 0.7377049 [132,] 178 407 48 48 11 37 0.7708333 [133,] 50 408 87 87 33 54 0.6206897 [134,] 55 421 118 117 31 85 0.7264957 [135,] 56 421 59 59 17 42 0.7118644 [136,] 79 421 124 124 11 113 0.9112903 [137,] 177 421 118 118 22 95 0.8050847 [138,] 6 422 107 107 27 79 0.7383178 [139,] 7 422 149 149 32 116 0.7785235 [140,] 50 441 62 62 22 40 0.6451613 [141,] 27 442 63 63 24 39 0.6190476 [142,] 124 444 69 69 15 54 0.7826087 [143,] 272 444 44 44 9 35 0.7954545 [144,] 50 446 52 52 20 32 0.6153846 [145,] 65 448 95 95 36 59 0.6210526 [146,] 66 448 112 112 37 74 0.6607143 [147,] 216 448 85 85 28 57 0.6705882 [148,] 46 449 113 113 38 74 0.6548673 [149,] 9 450 61 61 21 38 0.6229508 [150,] 10 450 58 58 20 36 0.6206897 [151,] 70 451 57 57 19 36 0.6315789 [152,] 34 454 41 41 10 31 0.7560976 [153,] 93 455 78 78 15 62 0.7948718 [154,] 13 460 136 136 50 85 0.6250000 [155,] 194 460 158 158 47 111 0.7025316 [156,] 80 461 99 99 26 73 0.7373737 [157,] 298 461 148 148 38 110 0.7432432 [158,] 2 464 88 88 34 53 0.6022727 [159,] 61 465 59 59 20 38 0.6440678 [160,] 95 466 55 55 16 38 0.6909091 [161,] 52 469 42 42 12 30 0.7142857 [162,] 101 469 47 47 12 35 0.7446809 [163,] 134 475 78 78 28 49 0.6282051 [164,] 152 475 49 49 16 32 0.6530612 [165,] 54 476 71 71 25 45 0.6338028 [166,] 256 476 43 43 17 26 0.6046512 [167,] 136 477 46 46 15 31 0.6739130 [168,] 141 484 43 43 13 30 0.6976744 [169,] 94 485 54 54 20 34 0.6296296 [170,] 3 489 156 155 46 107 0.6903226 [171,] 20 490 58 58 18 40 0.6896552 [172,] 87 490 73 73 29 44 0.6027397 [173,] 57 491 54 54 19 35 0.6481481 [174,] 60 503 77 77 22 55 0.7142857 [175,] 61 503 77 77 27 50 0.6493506 [176,] 28 508 42 42 16 26 0.6190476 [177,] 13 516 68 68 24 44 0.6470588 [178,] 194 516 82 82 25 57 0.6951220 [179,] 1 517 98 98 33 65 0.6632653 [180,] 21 520 76 76 18 58 0.7631579 [181,] 61 538 82 82 28 53 0.6463415 [182,] 176 538 50 50 19 31 0.6200000 [183,] 3 539 81 81 27 53 0.6543210 [184,] 9 539 89 89 32 57 0.6404494 [185,] 25 553 45 45 15 28 0.6222222 [186,] 133 554 42 42 11 30 0.7142857 [187,] 9 557 81 81 25 54 0.6666667 [188,] 27 557 86 86 28 57 0.6627907 [189,] 56 560 71 71 20 50 0.7042254 [190,] 39 561 45 45 9 36 0.8000000 [191,] 3 564 71 69 27 42 0.6086957 [192,] 265 565 46 46 14 32 0.6956522 [193,] 135 568 54 54 21 33 0.6111111 [194,] 62 580 46 46 15 30 0.6521739 [195,] 45 590 58 58 21 37 0.6379310 [196,] 119 591 45 45 15 30 0.6666667 [197,] 120 591 54 54 19 35 0.6481481 [198,] 32 600 85 85 26 57 0.6705882 [199,] 107 600 74 74 20 54 0.7297297 [200,] 8 601 89 89 25 62 0.6966292 [201,] 9 606 46 46 16 30 0.6521739 [202,] 79 606 45 45 15 29 0.6444444 [203,] 99 607 87 87 22 65 0.7471264 [204,] 104 607 55 55 20 35 0.6363636 [205,] 3 608 53 53 18 35 0.6603774 [206,] 6 608 92 92 26 65 0.7065217 [207,] 85 616 46 46 18 28 0.6086957 [208,] 70 618 61 61 13 48 0.7868852 [209,] 286 619 52 52 8 44 0.8461538 [210,] 96 620 41 41 12 28 0.6829268 [211,] 28 621 46 46 16 29 0.6304348 [212,] 59 625 49 49 17 32 0.6530612 [213,] 39 637 163 163 55 107 0.6564417 [214,] 139 637 107 107 34 73 0.6822430 [215,] 52 638 114 114 36 77 0.6754386 [216,] 100 638 161 161 53 107 0.6645963 [217,] 287 638 107 106 42 64 0.6037736 [218,] 293 638 48 48 15 33 0.6875000 [219,] 17 639 90 90 32 56 0.6222222 [220,] 222 639 104 104 40 63 0.6057692 > #denisT1: posAll <- 421 ibdC <- 79 #denisT2: posAll <- 132 ibdC <- 44 #denisT3: posAll <- 259 ibdC <- 67 #denisT4: !! posAll <- 619 ibdC <- 286 #denisT5: posAll <- 389 ibdC <- 9 #denisT6: !! posAll <- 96 ibdC <- 62 #denisT7: posAll <- 293 ibdC <- 33 #denisT8: !! posAll <- 561 ibdC <- 39 #denisT9: few asians !! posAll <- 444 ibdC <- 124 #denisT10: extrem oid !! posAll <- 372 ibdC <- 18 #denisT11: all populations no neander!! posAll <- 421 ibdC <- 55 #denisT12: denisova better with asian but africans have old posAll <- 503 ibdC <- 60 #denisT13: denisova in all populations posAll <- 422 ibdC <- 7 #denisT14: denisova in all populations posAll <- 608 ibdC <- 6 #denisT15: denisova in Africans !!!!!!!!!!!!!!!!!!!!!!!!! posAll <- 638 ibdC <- 100 #denisT16: denisova in Africans !! posAll <- 489 ibdC <- 3 #denisT17: denisova in Africans and Europeans !!!!!!!!!!!!!!!!!!!!! posAll <- 461 ibdC <- 298 > mergedIBD[[298]]$countrySamples [1] "GBR" "GBR" "GBR" "GBR" "GBR" "GBR" "GBR" "FIN" "GBR" "GBR" "GBR" "GBR" [13] "GBR" "FIN" "FIN" "FIN" "FIN" "FIN" "FIN" "FIN" "PUR" "PUR" "PUR" "PUR" [25] "CLM" "CLM" "CLM" "CLM" "CLM" "IBS" "CEU" "CEU" "CEU" "CEU" "CEU" "CEU" [37] "CEU" "CEU" "CEU" "CEU" "CEU" "CEU" "CEU" "YRI" "YRI" "YRI" "YRI" "YRI" [49] "YRI" "YRI" "YRI" "YRI" "YRI" "LWK" "LWK" "YRI" "YRI" "YRI" "YRI" "YRI" [61] "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "LWK" "LWK" [73] "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" [85] "LWK" "LWK" "MXL" "ASW" "ASW" "ASW" "ASW" "ASW" "ASW" "ASW" "TSI" "TSI" [97] "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" #denisT18: denisova in Africans and Asians but ancient posAll <- 132 ibdC <- 46 #denisT19: denisova in all populations but ancient posAll <- 517 ibdC <- 1 posAll <- 167 ibdC <- 32 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="denisT19" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ######################################################################### ######################################################################### ######################################################################### ne <- which(NeanderMat[,12]>0.6) nu <- which(NeanderMat[,5]>40) ns <- intersect(ne,nu) NeanderMat[ns,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 31 5 49 36 9 27 0.7500000 [2,] 53 6 46 36 12 23 0.6388889 [3,] 54 6 49 34 12 22 0.6470588 [4,] 133 6 44 31 9 22 0.7096774 [5,] 117 9 41 29 10 19 0.6551724 [6,] 107 10 43 31 11 19 0.6129032 [7,] 28 21 65 49 11 37 0.7551020 [8,] 69 21 42 28 7 21 0.7500000 [9,] 67 22 70 52 14 37 0.7115385 [10,] 5 28 43 28 8 20 0.7142857 [11,] 146 29 73 50 14 36 0.7200000 [12,] 147 29 61 47 16 31 0.6595745 [13,] 1 30 51 33 9 23 0.6969697 [14,] 2 30 73 47 11 35 0.7446809 [15,] 3 30 80 51 18 33 0.6470588 [16,] 52 31 46 31 8 22 0.7096774 [17,] 12 34 46 28 8 20 0.7142857 [18,] 13 34 46 32 5 27 0.8437500 [19,] 5 35 46 37 11 26 0.7027027 [20,] 27 36 43 29 8 19 0.6551724 [21,] 98 36 46 29 9 20 0.6896552 [22,] 57 37 233 136 42 94 0.6911765 [23,] 88 37 49 31 10 21 0.6774194 [24,] 190 37 266 157 59 97 0.6178344 [25,] 240 37 70 33 11 22 0.6666667 [26,] 5 38 257 159 58 100 0.6289308 [27,] 6 38 258 149 50 99 0.6644295 [28,] 66 39 72 46 17 28 0.6086957 [29,] 8 40 58 39 14 25 0.6410256 [30,] 46 41 77 50 16 34 0.6800000 [31,] 61 45 57 41 15 25 0.6097561 [32,] 94 52 49 35 8 27 0.7714286 [33,] 3 53 50 36 9 27 0.7500000 [34,] 5 53 45 31 9 22 0.7096774 [35,] 34 56 128 84 23 59 0.7023810 [36,] 47 56 67 50 14 34 0.6800000 [37,] 24 65 45 28 7 21 0.7500000 [38,] 124 88 62 41 14 27 0.6585366 [39,] 51 89 46 31 11 19 0.6129032 [40,] 59 89 49 30 8 22 0.7333333 [41,] 67 89 41 32 11 21 0.6562500 [42,] 297 89 51 34 10 24 0.7058824 [43,] 13 90 52 35 11 23 0.6571429 [44,] 33 91 53 35 11 23 0.6571429 [45,] 92 91 43 26 10 16 0.6153846 [46,] 62 96 42 25 4 21 0.8400000 [47,] 130 99 54 38 14 24 0.6315789 [48,] 24 106 87 68 16 51 0.7500000 [49,] 101 106 60 42 15 27 0.6428571 [50,] 114 106 55 43 9 33 0.7674419 [51,] 124 106 57 45 11 34 0.7555556 [52,] 119 107 61 48 14 34 0.7083333 [53,] 78 110 45 30 6 24 0.8000000 [54,] 145 123 43 27 8 19 0.7037037 [55,] 133 124 46 31 11 20 0.6451613 [56,] 78 131 125 96 29 66 0.6875000 [57,] 2 132 149 112 39 71 0.6339286 [58,] 1 136 55 34 13 21 0.6176471 [59,] 78 136 44 35 12 23 0.6571429 [60,] 108 136 57 37 14 23 0.6216216 [61,] 91 145 69 48 15 32 0.6666667 [62,] 2 146 55 40 13 26 0.6500000 [63,] 101 147 41 26 9 17 0.6538462 [64,] 238 148 41 29 9 20 0.6896552 [65,] 9 153 56 39 12 26 0.6666667 [66,] 72 154 55 39 13 25 0.6410256 [67,] 81 154 46 35 12 22 0.6285714 [68,] 5 155 44 34 12 21 0.6176471 [69,] 47 165 51 33 12 21 0.6363636 [70,] 5 166 82 54 13 41 0.7592593 [71,] 32 167 70 48 11 37 0.7708333 [72,] 108 171 76 44 16 28 0.6363636 [73,] 113 193 41 22 5 17 0.7727273 [74,] 12 202 66 39 14 24 0.6153846 [75,] 54 216 91 54 20 33 0.6111111 [76,] 9 217 86 51 17 33 0.6470588 [77,] 227 223 61 37 13 23 0.6216216 [78,] 10 224 42 18 5 13 0.7222222 [79,] 50 224 56 33 11 22 0.6666667 [80,] 38 234 43 24 8 16 0.6666667 [81,] 35 235 43 21 7 14 0.6666667 [82,] 38 235 52 27 5 22 0.8148148 [83,] 27 245 49 31 10 21 0.6774194 [84,] 5 246 50 27 8 19 0.7037037 [85,] 7 251 52 38 15 23 0.6052632 [86,] 32 259 54 26 10 16 0.6153846 [87,] 63 259 54 30 11 19 0.6333333 [88,] 66 259 51 30 8 22 0.7333333 [89,] 67 259 52 30 6 24 0.8000000 [90,] 6 260 46 26 10 16 0.6153846 [91,] 127 263 60 40 12 28 0.7000000 [92,] 72 264 56 37 9 28 0.7567568 [93,] 28 276 46 29 11 18 0.6206897 [94,] 100 276 54 34 11 23 0.6764706 [95,] 101 276 51 30 11 19 0.6333333 [96,] 61 280 61 34 10 24 0.7058824 [97,] 206 281 60 35 12 23 0.6571429 [98,] 54 287 140 92 26 66 0.7173913 [99,] 55 287 95 57 17 40 0.7017544 [100,] 139 288 42 16 6 10 0.6250000 [101,] 157 297 83 43 16 27 0.6279070 [102,] 254 305 46 17 2 15 0.8823529 [103,] 11 307 47 24 9 15 0.6250000 [104,] 115 325 50 28 8 20 0.7142857 [105,] 116 325 44 31 7 23 0.7419355 [106,] 4 326 45 32 7 24 0.7500000 [107,] 11 326 46 33 13 20 0.6060606 [108,] 13 326 48 30 10 20 0.6666667 [109,] 89 327 43 30 10 20 0.6666667 [110,] 91 327 43 26 7 19 0.7307692 [111,] 114 335 53 38 5 33 0.8684211 [112,] 9 346 106 73 22 50 0.6849315 [113,] 79 346 45 36 6 30 0.8333333 [114,] 3 347 68 49 14 35 0.7142857 [115,] 4 347 101 73 19 54 0.7397260 [116,] 5 347 90 59 19 39 0.6610169 [117,] 7 351 41 21 2 19 0.9047619 [118,] 11 351 61 48 18 30 0.6250000 [119,] 24 352 51 40 15 25 0.6250000 [120,] 24 356 78 52 17 33 0.6346154 [121,] 3 357 82 63 25 38 0.6031746 [122,] 32 358 53 40 14 26 0.6500000 [123,] 148 358 45 28 6 22 0.7857143 [124,] 173 359 46 28 6 22 0.7857143 [125,] 51 368 54 36 10 26 0.7222222 [126,] 14 372 55 42 16 26 0.6190476 [127,] 18 372 59 42 12 30 0.7142857 [128,] 103 373 60 43 13 30 0.6976744 [129,] 104 375 42 27 9 18 0.6666667 [130,] 35 376 42 27 9 18 0.6666667 [131,] 5 377 103 75 24 51 0.6800000 [132,] 31 378 108 78 27 51 0.6538462 [133,] 41 378 57 38 9 29 0.7631579 [134,] 8 379 70 50 13 37 0.7400000 [135,] 97 382 46 33 13 20 0.6060606 [136,] 10 383 41 29 9 20 0.6896552 [137,] 95 383 46 33 12 21 0.6363636 [138,] 96 383 64 37 12 25 0.6756757 [139,] 252 383 45 34 7 27 0.7941176 [140,] 19 384 50 38 6 32 0.8421053 [141,] 57 384 42 27 8 19 0.7037037 [142,] 65 384 47 33 12 21 0.6363636 [143,] 105 384 78 54 19 35 0.6481481 [144,] 84 385 76 49 19 30 0.6122449 [145,] 22 386 53 33 11 22 0.6666667 [146,] 87 387 42 29 9 20 0.6896552 [147,] 116 388 43 30 10 20 0.6666667 [148,] 8 389 112 64 23 41 0.6406250 [149,] 9 389 129 78 17 61 0.7820513 [150,] 68 390 56 40 14 26 0.6500000 [151,] 104 392 46 38 10 28 0.7368421 [152,] 123 393 42 29 9 20 0.6896552 [153,] 57 406 74 55 15 40 0.7272727 [154,] 58 406 44 28 9 19 0.6785714 [155,] 59 406 66 45 12 32 0.7111111 [156,] 61 406 41 27 7 20 0.7407407 [157,] 218 406 51 42 13 29 0.6904762 [158,] 1 407 75 56 16 40 0.7142857 [159,] 3 407 67 46 13 32 0.6956522 [160,] 4 407 58 34 8 26 0.7647059 [161,] 8 407 50 24 7 17 0.7083333 [162,] 175 407 52 43 14 29 0.6744186 [163,] 176 407 43 24 6 18 0.7500000 [164,] 180 407 55 34 12 22 0.6470588 [165,] 67 422 55 43 14 29 0.6744186 [166,] 233 422 43 31 11 20 0.6451613 [167,] 91 423 79 53 18 35 0.6603774 [168,] 144 423 52 41 13 28 0.6829268 [169,] 145 423 52 36 9 26 0.7222222 [170,] 6 424 71 46 17 29 0.6304348 [171,] 50 441 62 44 14 30 0.6818182 [172,] 27 442 63 45 13 32 0.7111111 [173,] 38 442 47 35 11 24 0.6857143 [174,] 225 442 67 44 13 31 0.7045455 [175,] 23 446 113 72 15 56 0.7777778 [176,] 92 446 97 57 14 42 0.7368421 [177,] 242 447 99 60 19 40 0.6666667 [178,] 65 448 95 49 18 30 0.6122449 [179,] 216 448 85 39 11 27 0.6923077 [180,] 9 450 61 39 12 27 0.6923077 [181,] 10 450 58 37 13 24 0.6486486 [182,] 11 450 78 49 17 32 0.6530612 [183,] 154 450 42 31 11 20 0.6451613 [184,] 10 451 56 36 11 25 0.6944444 [185,] 70 451 57 37 13 24 0.6486486 [186,] 71 451 75 48 16 32 0.6666667 [187,] 118 451 46 27 8 19 0.7037037 [188,] 119 451 108 54 13 41 0.7592593 [189,] 1 452 49 29 9 20 0.6896552 [190,] 2 452 78 38 11 27 0.7105263 [191,] 13 452 71 48 14 34 0.7083333 [192,] 222 452 81 36 4 32 0.8888889 [193,] 11 454 66 45 15 29 0.6444444 [194,] 12 454 56 31 9 22 0.7096774 [195,] 8 463 79 43 13 30 0.6976744 [196,] 9 463 79 43 13 29 0.6744186 [197,] 1 464 50 26 7 19 0.7307692 [198,] 2 464 88 50 15 35 0.7000000 [199,] 289 464 47 24 6 17 0.7083333 [200,] 61 465 59 40 11 28 0.7000000 [201,] 154 465 62 33 10 23 0.6969697 [202,] 95 466 55 37 8 28 0.7567568 [203,] 101 469 47 28 9 19 0.6785714 [204,] 4 470 90 46 13 32 0.6956522 [205,] 147 470 55 35 13 22 0.6285714 [206,] 14 471 94 48 15 32 0.6666667 [207,] 75 471 71 40 15 25 0.6250000 [208,] 17 472 43 26 8 18 0.6923077 [209,] 67 479 48 28 11 17 0.6071429 [210,] 127 483 45 22 6 16 0.7272727 [211,] 49 484 50 28 7 21 0.7500000 [212,] 95 484 49 30 9 21 0.7000000 [213,] 141 484 43 21 8 13 0.6190476 [214,] 86 485 48 31 10 21 0.6774194 [215,] 94 485 54 29 10 19 0.6551724 [216,] 39 486 42 23 5 18 0.7826087 [217,] 52 487 41 23 9 14 0.6086957 [218,] 95 489 41 25 4 20 0.8000000 [219,] 2 490 42 26 5 20 0.7692308 [220,] 20 490 58 37 8 29 0.7837838 [221,] 51 491 78 40 12 27 0.6750000 [222,] 57 491 54 35 9 26 0.7428571 [223,] 64 491 78 40 12 27 0.6750000 [224,] 236 491 73 41 12 28 0.6829268 [225,] 68 492 79 40 12 27 0.6750000 [226,] 79 492 44 24 5 19 0.7916667 [227,] 204 492 74 42 13 28 0.6666667 [228,] 210 495 88 58 22 36 0.6206897 [229,] 28 496 42 24 7 17 0.7083333 [230,] 29 496 42 27 7 20 0.7407407 [231,] 30 496 42 25 7 18 0.7200000 [232,] 139 505 43 37 12 25 0.6756757 [233,] 127 506 42 36 11 25 0.6944444 [234,] 26 508 55 43 15 28 0.6511628 [235,] 27 508 53 37 10 26 0.7027027 [236,] 28 508 42 30 7 23 0.7666667 [237,] 11 509 47 37 13 24 0.6486486 [238,] 16 509 43 32 6 26 0.8125000 [239,] 54 509 54 40 12 28 0.7000000 [240,] 85 512 55 40 11 28 0.7000000 [241,] 66 515 45 29 8 21 0.7241379 [242,] 67 515 42 23 6 17 0.7391304 [243,] 13 516 68 45 16 29 0.6444444 [244,] 1 517 98 63 25 38 0.6031746 [245,] 96 519 43 26 10 16 0.6153846 [246,] 12 520 43 26 10 16 0.6153846 [247,] 21 520 76 46 14 32 0.6956522 [248,] 35 530 75 55 19 35 0.6363636 [249,] 63 530 87 55 19 36 0.6545455 [250,] 62 531 74 54 18 35 0.6481481 [251,] 21 534 84 54 20 34 0.6296296 [252,] 80 534 51 27 6 21 0.7777778 [253,] 2 535 82 53 19 34 0.6415094 [254,] 121 535 59 33 12 21 0.6363636 [255,] 61 537 42 26 7 19 0.7307692 [256,] 67 537 48 25 7 18 0.7200000 [257,] 35 538 43 27 4 23 0.8518519 [258,] 61 538 82 54 20 34 0.6296296 [259,] 64 538 52 30 10 20 0.6666667 [260,] 2 539 64 43 16 26 0.6046512 [261,] 3 539 81 53 19 34 0.6415094 [262,] 6 539 47 27 7 20 0.7407407 [263,] 9 539 89 53 13 40 0.7547170 [264,] 15 545 62 27 8 19 0.7037037 [265,] 20 545 59 35 11 24 0.6857143 [266,] 10 546 67 26 10 16 0.6153846 [267,] 15 546 48 28 8 20 0.7142857 [268,] 11 548 43 28 11 17 0.6071429 [269,] 33 548 70 42 13 28 0.6666667 [270,] 34 548 71 39 10 29 0.7435897 [271,] 35 548 41 21 8 13 0.6190476 [272,] 3 549 70 43 14 28 0.6511628 [273,] 4 549 81 45 10 35 0.7777778 [274,] 45 550 41 20 7 13 0.6500000 [275,] 137 553 47 30 10 20 0.6666667 [276,] 15 554 254 144 54 90 0.6250000 [277,] 39 554 182 98 37 61 0.6224490 [278,] 40 554 58 35 13 22 0.6285714 [279,] 60 554 52 32 11 21 0.6562500 [280,] 61 554 56 41 14 27 0.6585366 [281,] 63 554 43 28 9 18 0.6428571 [282,] 66 554 102 69 25 44 0.6376812 [283,] 74 554 59 44 16 27 0.6136364 [284,] 77 554 44 25 6 19 0.7600000 [285,] 114 554 96 64 18 46 0.7187500 [286,] 132 554 46 28 8 20 0.7142857 [287,] 133 554 42 30 9 21 0.7000000 [288,] 242 554 111 73 25 47 0.6438356 [289,] 7 555 118 77 30 47 0.6103896 [290,] 76 555 41 35 7 27 0.7714286 [291,] 77 555 41 33 11 22 0.6666667 [292,] 125 555 46 28 7 21 0.7500000 [293,] 241 555 101 68 21 46 0.6764706 [294,] 39 556 104 73 24 49 0.6712329 [295,] 23 557 58 38 4 34 0.8947368 [296,] 26 557 99 67 20 47 0.7014925 [297,] 27 557 86 63 15 48 0.7619048 [298,] 200 557 44 28 6 22 0.7857143 [299,] 34 558 69 45 8 37 0.8222222 [300,] 39 561 45 28 9 19 0.6785714 [301,] 88 565 51 39 15 24 0.6153846 [302,] 90 565 47 32 11 21 0.6562500 [303,] 265 565 46 36 8 28 0.7777778 [304,] 17 566 48 33 12 21 0.6363636 [305,] 48 571 80 60 18 42 0.7000000 [306,] 129 573 54 39 14 24 0.6153846 [307,] 130 573 41 29 10 19 0.6551724 [308,] 27 574 50 37 11 26 0.7027027 [309,] 61 575 54 41 16 25 0.6097561 [310,] 92 577 51 38 12 26 0.6842105 [311,] 64 589 41 28 8 20 0.7142857 [312,] 66 589 58 41 16 25 0.6097561 [313,] 42 590 49 30 11 19 0.6333333 [314,] 43 590 56 43 15 26 0.6046512 [315,] 45 590 58 42 15 27 0.6428571 [316,] 119 591 45 28 9 19 0.6785714 [317,] 120 591 54 39 13 26 0.6666667 [318,] 57 600 54 34 11 23 0.6764706 [319,] 40 604 58 36 13 22 0.6111111 [320,] 79 606 45 22 8 14 0.6363636 [321,] 70 618 61 38 14 24 0.6315789 [322,] 286 619 52 31 11 20 0.6451613 [323,] 90 629 80 58 15 43 0.7413793 > # neanderT1: European with some Africans posAll <- 34 ibdC <- 13 # neanderT2: neandertal haplotype of Europeans posAll <- 346 ibdC <- 79 # neanderT3: neandertal haplotype of Europeans posAll <- 351 ibdC <- 7 # neanderT4: neandertal haplotype of Africans with Fins overlap posAll <- 446 ibdC <- 23 # neanderT5: neandertal haplotype of Fins and Asians posAll <- 452 ibdC <- 222 # neanderT6: neandertal haplotype of Asians posAll <- 486 ibdC <- 39 # neanderT7: neandertal haplotype of Asians and Europeans posAll <- 538 ibdC <- 35 # neanderT8: neandertal haplotype of all populations posAll <- 554 ibdC <- 15 > mergedIBD[[15]]$countrySamples [1] "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" "CHS" [13] "CHS" "CHS" "PUR" "CLM" "CLM" "IBS" "IBS" "IBS" "YRI" "YRI" "YRI" "YRI" [25] "YRI" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" [37] "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" "CHB" [49] "CHB" "YRI" "YRI" "YRI" "YRI" "YRI" "YRI" "JPT" "JPT" "JPT" "JPT" "JPT" [61] "JPT" "JPT" "LWK" "LWK" "JPT" "JPT" "JPT" "JPT" "YRI" "YRI" "YRI" "YRI" [73] "YRI" "YRI" "YRI" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" [85] "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" "LWK" [97] "LWK" "LWK" "ASW" "ASW" "MXL" "ASW" "ASW" "ASW" "ASW" "ASW" "ASW" "ASW" [109] "ASW" "ASW" "ASW" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" "TSI" # neanderT9: neandertal haplotype of Africans posAll <- 629 ibdC <- 90 posAll <- 347 ibdC <- 4 start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name="neanderT9" pdf(paste(name,".pdf",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotoneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() ######################################################################### ######################################################################### ######################################################################### ae <- which(AncestMat[,12]>0.5) au <- which(AncestMat[,5]>40) as <- intersect(ae,au) AncestMat[as,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 223 1 42 1 0 1 1.0000000 [2,] 8 20 53 45 21 24 0.5333333 [3,] 116 48 43 9 3 6 0.6666667 [4,] 19 49 45 11 4 7 0.6363636 [5,] 171 74 59 42 19 23 0.5476190 [6,] 17 93 57 57 16 41 0.7192982 [7,] 65 94 65 61 25 36 0.5901639 [8,] 66 94 52 52 16 35 0.6730769 [9,] 230 148 41 41 17 24 0.5853659 [10,] 140 149 49 49 22 27 0.5510204 [11,] 66 178 44 44 20 24 0.5454545 [12,] 36 210 87 85 42 43 0.5058824 [13,] 2 211 86 84 41 43 0.5119048 [14,] 20 211 56 56 27 29 0.5178571 [15,] 198 226 80 80 39 41 0.5125000 [16,] 13 227 53 48 22 26 0.5416667 [17,] 78 254 45 45 14 31 0.6888889 [18,] 78 255 46 46 15 31 0.6739130 [19,] 26 258 59 58 21 36 0.6206897 [20,] 30 259 58 57 20 36 0.6315789 [21,] 32 259 54 53 17 36 0.6792453 [22,] 63 259 54 47 22 25 0.5319149 [23,] 66 259 51 51 12 39 0.7647059 [24,] 67 259 52 52 11 41 0.7884615 [25,] 6 260 46 46 20 26 0.5652174 [26,] 7 260 55 48 17 31 0.6458333 [27,] 127 263 60 57 22 35 0.6140351 [28,] 37 264 44 41 19 22 0.5365854 [29,] 72 264 56 52 21 31 0.5961538 [30,] 51 274 49 49 23 26 0.5306122 [31,] 220 295 60 60 21 38 0.6333333 [32,] 110 296 74 74 33 39 0.5270270 [33,] 41 304 41 41 20 21 0.5121951 [34,] 11 306 51 51 18 33 0.6470588 [35,] 11 307 47 47 17 30 0.6382979 [36,] 64 307 74 73 33 37 0.5068493 [37,] 31 337 50 50 22 28 0.5600000 [38,] 146 342 42 26 11 15 0.5769231 [39,] 33 343 42 38 15 22 0.5789474 [40,] 12 344 55 23 9 14 0.6086957 [41,] 177 348 46 7 3 4 0.5714286 [42,] 55 354 51 51 23 28 0.5490196 [43,] 24 373 51 38 17 21 0.5526316 [44,] 103 373 60 60 28 32 0.5333333 [45,] 137 373 43 43 16 26 0.6046512 [46,] 6 385 41 41 18 23 0.5609756 [47,] 63 406 52 52 22 30 0.5769231 [48,] 221 406 60 60 27 33 0.5500000 [49,] 79 421 124 124 55 67 0.5403226 [50,] 94 423 61 61 26 35 0.5737705 [51,] 97 423 74 73 36 37 0.5068493 [52,] 266 423 68 68 26 42 0.6176471 [53,] 73 424 49 49 22 27 0.5510204 [54,] 223 424 68 68 26 42 0.6176471 [55,] 125 434 47 47 22 25 0.5319149 [56,] 109 436 46 44 21 23 0.5227273 [57,] 34 454 41 41 15 25 0.6097561 [58,] 93 455 78 77 29 48 0.6233766 [59,] 298 461 148 148 71 75 0.5067568 [60,] 52 469 42 42 16 26 0.6190476 [61,] 101 469 47 47 16 31 0.6595745 [62,] 108 477 62 60 27 31 0.5166667 [63,] 136 477 46 44 14 30 0.6818182 [64,] 29 478 57 55 25 29 0.5272727 [65,] 95 478 49 47 19 28 0.5957447 [66,] 25 553 45 45 22 23 0.5111111 [67,] 62 580 46 45 20 25 0.5555556 [68,] 85 616 46 46 21 25 0.5434783 [69,] 59 625 49 49 18 31 0.6326531 [70,] 90 629 80 80 32 48 0.6000000 > # ancestT1: shift <- 5000 intervallAll <- 10000 lengthAll <- 3201157 tn <- which(AncestMat[,5]>100) ibdCA <- AncestMat[tn,3] posAllA <- AncestMat[tn,4] ibdCA <- c(51,57,190,9,5,39,60,53) posAllA <- c(26,37,37,39,40,45,131,143) for (i in 1:length(tn)) { posAll <-posAllA[i] ibdC <- ibdCA[i] start <- (posAll-1)*shift end <- start + intervallAll if (end > lengthAll) { end <- lengthAll } pRange <- paste("_",format(start,scientific=FALSE),"_",format(end,scientific=FALSE),sep="") load(file=paste("resIBD_chr1",pRange,".Rda",sep="")) plotOneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) name=paste("example",i,sep="") pdf(paste(name,".pdf",sep=""),width=12) plotOneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() xfig(paste(name,".fig",sep=""),width=12) plotOneIBD(mergedIBD,paste("../ALL.chr1.merged_beagle_mach.20101123.snps_indels_svs.genotypes",pRange,"_mat",sep=""),ibdC) dev.off() } [7,] 88 25 113 111 81 30 0.27027027 [8,] 31 26 114 114 70 44 0.38596491 [9,] 51 26 126 125 85 40 0.32000000 [10,] 8 29 111 110 79 31 0.28181818 [11,] 9 29 114 112 78 32 0.28571429 [15,] 57 37 233 0 0 0 0.00000000 [17,] 190 37 266 0 0 0 0.00000000 [20,] 9 39 150 150 103 46 0.30666667 [21,] 5 40 123 123 80 42 0.34146341 [24,] 36 41 103 103 73 30 0.29126214 [30,] 39 45 118 117 84 33 0.28205128 [35,] 34 56 128 112 76 35 0.31250000 [49,] 123 89 118 116 71 43 0.37068966 [69,] 5 130 102 100 75 25 0.25000000 [70,] 39 131 116 112 77 34 0.30357143 [72,] 60 131 157 153 106 47 0.30718954 [87,] 53 143 160 160 113 46 0.28750000 tn <- which(AncestMat[,5]>100) AncestMat[tn,c(3:8,12)] ibdC posAll #SNPs #Nea #Ref #Alt AltR [1,] 94 7 111 110 81 28 0.25454545 [2,] 21 15 103 103 92 9 0.08737864 [3,] 6 16 107 80 57 22 0.27500000 [4,] 27 16 110 110 100 8 0.07272727 [5,] 16 25 120 120 103 17 0.14166667 [6,] 86 25 129 129 77 52 0.40310078 [7,] 88 25 113 111 81 30 0.27027027 [8,] 31 26 114 114 70 44 0.38596491 [9,] 51 26 126 125 85 40 0.32000000 [10,] 8 29 111 110 79 31 0.28181818 [11,] 9 29 114 112 78 32 0.28571429 [12,] 30 30 101 98 87 11 0.11224490 [13,] 24 36 108 108 84 24 0.22222222 [14,] 56 37 212 0 0 0 0.00000000 [15,] 57 37 233 0 0 0 0.00000000 [16,] 158 37 144 0 0 0 0.00000000 [17,] 190 37 266 0 0 0 0.00000000 [18,] 5 38 257 0 0 0 0.00000000 [19,] 6 38 258 0 0 0 0.00000000 [20,] 9 39 150 150 103 46 0.30666667 [21,] 5 40 123 123 80 42 0.34146341 [22,] 97 40 145 145 109 36 0.24827586 [23,] 11 41 131 131 98 33 0.25190840 [24,] 36 41 103 103 73 30 0.29126214 [25,] 20 42 102 102 69 33 0.32352941 [26,] 57 43 117 113 83 30 0.26548673 [27,] 18 44 144 138 100 38 0.27536232 [28,] 54 44 123 123 85 38 0.30894309 [29,] 1 45 124 124 86 38 0.30645161 [30,] 39 45 118 117 84 33 0.28205128 [31,] 40 45 101 101 74 26 0.25742574 [32,] 9 46 120 119 86 33 0.27731092 [33,] 89 49 102 86 68 17 0.19767442 [34,] 1 51 108 105 84 21 0.20000000 [35,] 34 56 128 112 76 35 0.31250000 [36,] 22 69 114 114 82 32 0.28070175 [37,] 7 70 114 114 80 34 0.29824561 [38,] 37 70 107 107 75 32 0.29906542 [39,] 14 71 184 182 115 64 0.35164835 [40,] 132 71 160 158 93 63 0.39873418 [41,] 5 72 175 172 106 63 0.36627907 [42,] 60 73 147 125 88 35 0.28000000 [43,] 78 73 130 124 92 32 0.25806452 [44,] 7 74 151 145 111 34 0.23448276 [45,] 8 74 144 114 77 35 0.30701754 [46,] 52 77 101 98 69 28 0.28571429 [47,] 44 78 106 103 76 25 0.24271845 [48,] 78 81 111 110 90 20 0.18181818 [49,] 123 89 118 116 71 43 0.37068966 [50,] 6 90 130 129 78 49 0.37984496 [51,] 35 92 102 100 85 15 0.15000000 [52,] 58 93 105 100 77 23 0.23000000 [53,] 206 93 104 96 78 18 0.18750000 [54,] 94 94 103 103 82 21 0.20388350 [55,] 18 101 135 135 104 31 0.22962963 [56,] 31 101 103 96 83 13 0.13541667 [57,] 63 101 121 120 85 35 0.29166667 [58,] 249 101 125 125 96 28 0.22400000 [59,] 15 102 114 114 80 33 0.28947368 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156 115 78 36 0.31304348 [87,] 53 143 160 160 113 46 0.28750000 [88,] 9 144 124 124 91 33 0.26612903 [89,] 10 144 122 122 71 51 0.41803279 [90,] 27 144 148 148 108 39 0.26351351 [91,] 75 144 108 108 57 51 0.47222222 [92,] 33 145 118 118 66 52 0.44067797 [93,] 34 145 110 104 66 37 0.35576923 [94,] 20 151 141 141 103 36 0.25531915 [95,] 191 152 110 110 76 32 0.29090909 [96,] 12 165 102 102 83 19 0.18627451 [97,] 12 166 123 123 102 21 0.17073171 [98,] 23 167 158 158 109 49 0.31012658 [99,] 39 168 143 143 95 48 0.33566434 [100,] 51 168 101 100 79 21 0.21000000 [101,] 111 168 107 107 85 22 0.20560748 [102,] 71 169 118 118 86 30 0.25423729 [103,] 103 169 106 106 84 22 0.20754717 [104,] 12 170 116 116 83 32 0.27586207 [105,] 60 170 106 106 80 26 0.24528302 [106,] 13 171 108 108 82 26 0.24074074 [107,] 49 176 104 101 78 22 0.21782178 [108,] 32 182 103 103 66 37 0.35922330 [109,] 64 198 106 105 88 17 0.16190476 [110,] 65 201 110 110 74 34 0.30909091 [111,] 85 202 109 109 73 34 0.31192661 [112,] 119 202 107 106 75 30 0.28301887 [113,] 51 203 108 106 82 21 0.19811321 [114,] 5 204 107 106 78 26 0.24528302 [115,] 14 204 102 100 67 32 0.32000000 [116,] 12 205 178 178 149 28 0.15730337 [117,] 13 206 170 165 102 62 0.37575758 [118,] 7 207 169 163 100 62 0.38036810 [119,] 10 207 114 113 73 39 0.34513274 [120,] 48 207 143 142 95 47 0.33098592 [121,] 1 208 108 107 73 34 0.31775701 [122,] 131 208 105 105 66 38 0.36190476 [123,] 64 211 104 102 74 28 0.27450980 [124,] 124 211 145 144 86 57 0.39583333 [125,] 14 212 103 102 60 41 0.40196078 [126,] 38 212 153 152 88 63 0.41447368 [127,] 29 223 119 119 92 26 0.21848739 [128,] 50 225 150 146 84 61 0.41780822 [129,] 7 226 145 142 82 59 0.41549296 [130,] 12 227 104 104 71 32 0.30769231 [131,] 46 227 101 101 63 37 0.36633663 [132,] 15 228 121 121 82 38 0.31404959 [133,] 40 229 172 172 114 58 0.33720930 [134,] 56 229 118 118 82 35 0.29661017 [135,] 4 230 170 170 112 57 0.33529412 [136,] 9 230 125 125 87 37 0.29600000 [137,] 61 230 108 108 75 33 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[189,] 60 317 104 104 81 23 0.22115385 [190,] 95 317 135 134 77 57 0.42537313 [191,] 24 321 102 94 74 20 0.21276596 [192,] 136 321 103 82 56 26 0.31707317 [193,] 291 321 105 85 63 22 0.25882353 [194,] 8 322 102 86 75 11 0.12790698 [195,] 98 322 126 106 82 24 0.22641509 [196,] 257 322 125 99 75 24 0.24242424 [197,] 135 330 102 101 59 41 0.40594059 [198,] 12 335 124 124 71 53 0.42741935 [199,] 2 336 125 125 72 53 0.42400000 [200,] 11 338 137 137 94 43 0.31386861 [201,] 12 338 189 181 130 51 0.28176796 [202,] 106 338 124 118 82 36 0.30508475 [203,] 168 338 184 178 119 59 0.33146067 [204,] 53 339 171 165 119 46 0.27878788 [205,] 80 339 224 218 148 70 0.32110092 [206,] 29 344 110 47 35 12 0.25531915 [207,] 47 344 127 0 0 0 0.00000000 [208,] 71 344 147 42 28 14 0.33333333 [209,] 88 345 137 7 5 2 0.28571429 [210,] 225 345 130 40 26 14 0.35000000 [211,] 9 346 106 103 72 29 0.28155340 [212,] 4 347 101 100 71 28 0.28000000 [213,] 34 347 150 128 87 40 0.31250000 [214,] 7 348 123 103 66 36 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