The fields of DenisovaMat, DenisovaMat, and AncestMat:
[1] "allCount1" "allCount" "ibdC"
[4] "posAll" "#SNPs" "#Nea"
[7] "#Ref" "#Alt" "#New"
[10] "NeaR" "RefR" "AltR"
[13] "NewR" "xAltCon" "xRefCon"
[16] "mAltCon" "mRefCon" "NeaPosC"
[19] "AltPosC" "RefPosC" "IBDlength"
[22] "IBDlengthCorrected" "#samples" "AFR"
[25] "AMR" "ASN" "EUR"
[28] "AFRr" "AMRr" "ASNr"
[31] "EURr" "IBDlengthNew" "ancientLengthSNVs"
[34] "ancientLength" "ancientRatio"
"allCount1" Non redundant IBD segment count
"allCount" count with redundant IBD segments removed
"ibdC" Number of IBD segments in this interval
"posAll" Number of the current interval
"#SNPs" Number of tagSNVs
"#Nea" Number of SNVs called in archaic genome (of tagSNVs)
"#Ref" Number of SNVs matching human reference
"#Alt" Number of SNVs matching human alternative (minor human)
"#New" Number of SNVs that are different from human (major, minor)
"NeaR" Ratio of SNVs called in archaic genome
"RefR" Ratio of SNVs matching human reference
"AltR" Ratio of SNVs matchin human alternative (minor)
"NewR" Ratio of SNVs that are different from human (major, minor)
"xAltCon" median distance between matched (archaic-human) positions (minor human)
"xRefCon" median distance of reference positions (major human)
"mAltCon" mean distance between matched positions (minor human)
"mRefCon" mean distance between reference positions (major human)
"NeaPosC" median physical distance between tagSNV positions
"AltPosC" median physical distance between matched positions (minor human)
"RefPosC" median physical distance between reference positions (major human)
"IBDlength" length of IBD segment (maximum)
"IBDlengthCorrected" length of IBD segment corrected (3/4 of chromosomes match)
"#samples" number of samples with this IBD segment
"AFR" number of Africans
"AMR" number of admixed Americans
"ASN" number of Asians
"EUR" number of Europeans
"AFRr" ratio of Africans
"AMRr" ratio of admixed Americans
"ASNr" ratio of Asians
"EURr" ratio of Europeans
"IBDlengthNew" length of IBD (same as IBDlength)
"ancientLengthSNVs" number of tagSNVs in archaic part - 1 (note the -1 !)
"ancientLength" length of archaic part
"ancientRatio" ratio of matching tagSNVs in archaic part
NOTE: archaic or ancient refers always to the genome that is
indicated by the filename
###########
The fields of PopulationMat:
[1] "allCount1" "allCount" "ibdC" "posAll" "#Samples" "AFR"
[7] "AMR" "ASN" "EUR"
"allCount1" Non redundant IBD segment count
"allCount" count with redundant IBD segments removed
"ibdC" Number of IBD segments in this interval
"posAll" Number of the current interval
"#Samples" Number of samples
"AFR" ratio of Africans
"AMR" ratio of admixed Americans
"ASN" ratio of Asians
"EUR" ratio of Europeans
###############################################
LLL <- DenisovaMat[,22]
LLLZ <- which(LLL>10)
LLL <- LLL[LLLZ]
de <- intersect(de1,de2)
DE <- intersect(DE1,DE2)
ne <- intersect(ne1,ne2)
NE <- intersect(NE1,NE2)
dene <- intersect(de,ne)
de <- setdiff(de,dene)
ne <- setdiff(ne,dene)
DENE <- intersect(DE,NE)
DE <- setdiff(DE,DENE)
NE <- setdiff(NE,DENE)
AFR <- which(PopulationMat[,6]>0.2) #147574
ASN <- which(PopulationMat[,8]>0.2) #7472
EUR <- which(PopulationMat[,9]>0.2) #10688
AFRd <- which(PopulationMat[,6]>0.5) #141262
ASNd <- which(PopulationMat[,8]>0.5) #5161
EURd <- which(PopulationMat[,9]>0.5) #5915
LLLAFR <- DenisovaMat[AFR,22]
LLLASN <- DenisovaMat[ASN,22]
LLLEUR <- DenisovaMat[EUR,22]
LLLAFRd <- DenisovaMat[AFRd,22]
LLLASNd <- DenisovaMat[ASNd,22]
LLLEURd <- DenisovaMat[EURd,22]
neL <- NeanderMat[ne,34]
deL <- DenisovaMat[de,34]
deneL <- DenisovaMat[dene,34]
NEL <- NeanderMat[NE,34]
DEL <- DenisovaMat[DE,34]
DENEL <- DenisovaMat[dene,34]
> summary(DenisovaMat[,21])
Min. 1st Qu. Median Mean 3rd Qu. Max.
56 20120 25380 26970 30550 21250000
> summary(DenisovaMat[,22])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 17610 23250 23950 28410 21250000
Corrected:
> summary(LLL)
Min. 1st Qu. Median Mean 3rd Qu. Max.
34 17860 23360 24220 28480 21250000
> summary(deL)
Min. 1st Qu. Median Mean 3rd Qu. Max.
252 7340 12830 15570 20700 291900
> summary(neL)
Min. 1st Qu. Median Mean 3rd Qu. Max.
509 13600 20150 21220 26860 331300
> summary(deneL)
Min. 1st Qu. Median Mean 3rd Qu. Max.
435 10740 18250 19560 26090 314100
> summary(DenisovaMat[,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 0 0 1102 0 314100
> summary(NeanderMat[,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 0 0 1963 0 331300
> shorT <- which(DenisovaMat[,5]==9)
> shorTL <- DenisovaMat[shorT,22]
> summary(shorTL)
Min. 1st Qu. Median Mean 3rd Qu. Max.
56 15820 21260 21700 26260 595000
de1 <- which(DenisovaMat[,12]>0.15)
de2 <- which(DenisovaMat[,35]>0.3)
de <- intersect(de1,de2)
DE1 <- which(DenisovaMat[,12]>0.3)
DE2 <- which(DenisovaMat[,35]>0.6)
DE <- intersect(DE1,DE2)
ne1 <- which(NeanderMat[,12]>0.15)
ne2 <- which(NeanderMat[,35]>0.3)
ne <- intersect(ne1,ne2)
NE1 <- which(NeanderMat[,12]>0.3)
NE2 <- which(NeanderMat[,35]>0.6)
NE <- intersect(NE1,NE2)
dene <- intersect(de,ne)
de <- setdiff(de,dene)
ne <- setdiff(ne,dene)
DENE <- intersect(DE,NE)
DE <- setdiff(DE,DENE)
NE <- setdiff(NE,DENE)
> length(ne)
[1] 8173
> length(de)
[1] 4005
> length(dene)
[1] 5606
summary(DenisovaMat[de,5])
summary(DenisovaMat[de,23])
summary(DenisovaMat[de,22])
summary(DenisovaMat[de,33])
summary(DenisovaMat[de,34])
summary(DenisovaMat[de,35])
> summary(DenisovaMat[de,5])
Min. 1st Qu. Median Mean 3rd Qu. Max.
9.00 14.00 25.00 32.06 41.00 164.00
> summary(DenisovaMat[de,23])
Min. 1st Qu. Median Mean 3rd Qu. Max.
2.00 7.00 18.00 28.21 41.00 163.00
> summary(DenisovaMat[de,22])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 13050 21520 21740 28710 337800
> summary(DenisovaMat[de,33])
Min. 1st Qu. Median Mean 3rd Qu. Max.
6.00 8.00 10.00 17.06 17.00 161.00
> summary(DenisovaMat[de,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
252 7340 12830 15570 20700 291900
> summary(DenisovaMat[de,35])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.3051 0.5000 0.5625 0.5925 0.6667 1.0000
summary(NeanderMat[ne,5])
summary(NeanderMat[ne,23])
summary(NeanderMat[ne,22])
summary(NeanderMat[ne,33])
summary(NeanderMat[ne,34])
summary(NeanderMat[ne,35])
> summary(NeanderMat[ne,5])
Min. 1st Qu. Median Mean 3rd Qu. Max.
9.00 11.00 16.00 21.53 25.00 254.00
> summary(NeanderMat[ne,23])
Min. 1st Qu. Median Mean 3rd Qu. Max.
2.00 5.00 16.00 24.84 36.00 151.00
> summary(NeanderMat[ne,22])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 16570 23260 23340 29200 410100
> summary(NeanderMat[ne,33])
Min. 1st Qu. Median Mean 3rd Qu. Max.
6.00 8.00 10.00 15.22 15.00 251.00
> summary(NeanderMat[ne,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
509 13600 20150 21220 26860 331300
> summary(NeanderMat[ne,35])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.3462 0.6667 0.7284 0.7350 0.8000 1.0000
>
summary(DenisovaMat[dene,5])
summary(DenisovaMat[dene,23])
summary(DenisovaMat[dene,22])
summary(NeanderMat[dene,33])
summary(DenisovaMat[dene,33])
summary(NeanderMat[dene,34])
summary(DenisovaMat[dene,34])
summary(NeanderMat[dene,35])
summary(DenisovaMat[dene,35])
> summary(DenisovaMat[dene,5])
Min. 1st Qu. Median Mean 3rd Qu. Max.
9.00 15.00 25.00 32.95 42.00 266.00
> summary(DenisovaMat[dene,23])
Min. 1st Qu. Median Mean 3rd Qu. Max.
2.0 10.0 26.0 34.4 51.0 176.0
> summary(DenisovaMat[dene,22])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0 14060 23100 22840 30120 318600
> summary(NeanderMat[dene,33])
Min. 1st Qu. Median Mean 3rd Qu. Max.
6.00 10.00 15.00 23.82 30.00 264.00
> summary(DenisovaMat[dene,33])
Min. 1st Qu. Median Mean 3rd Qu. Max.
6.00 9.00 13.00 21.17 25.00 263.00
> summary(NeanderMat[dene,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
666 14430 22190 23240 29730 310300
> summary(DenisovaMat[dene,34])
Min. 1st Qu. Median Mean 3rd Qu. Max.
435 10740 18250 19560 26090 314100
> summary(NeanderMat[dene,35])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.3846 0.6667 0.7449 0.7414 0.8182 1.0000
> summary(DenisovaMat[dene,35])
Min. 1st Qu. Median Mean 3rd Qu. Max.
0.3023 0.5263 0.6222 0.6387 0.7500 1.0000
summary(DenisovaMat[de,24:31])
summary(NeanderMat[ne,24:31])
summary(DenisovaMat[dene,24:31])
> summary(DenisovaMat[de,24:31])
AFR AMR ASN EUR
Min. : 0.00 Min. : 0.000 Min. : 0.000 Min. : 0.00
1st Qu.: 4.00 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.00
Median : 13.00 Median : 1.000 Median : 0.000 Median : 0.00
Mean : 21.52 Mean : 2.158 Mean : 2.321 Mean : 2.21
3rd Qu.: 31.00 3rd Qu.: 3.000 3rd Qu.: 0.000 3rd Qu.: 0.00
Max. :149.00 Max. :37.000 Max. :83.000 Max. :79.00
AFRr AMRr ASNr EURr
Min. :0.0000 Min. :0.00000 Min. :0.00000 Min. :0.00000
1st Qu.:0.8000 1st Qu.:0.00000 1st Qu.:0.00000 1st Qu.:0.00000
Median :0.9286 Median :0.04225 Median :0.00000 Median :0.00000
Mean :0.7797 Mean :0.06653 Mean :0.09793 Mean :0.05586
3rd Qu.:1.0000 3rd Qu.:0.09091 3rd Qu.:0.00000 3rd Qu.:0.00000
Max. :1.0000 Max. :1.00000 Max. :1.00000 Max. :1.00000
> summary(NeanderMat[ne,24:31])
AFR AMR ASN EUR
Min. : 0.000 Min. : 0.000 Min. : 0.000 Min. : 0.000
1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.000
Median : 3.000 Median : 1.000 Median : 0.000 Median : 0.000
Mean : 9.681 Mean : 3.114 Mean : 5.879 Mean : 6.166
3rd Qu.: 12.000 3rd Qu.: 4.000 3rd Qu.: 5.000 3rd Qu.: 5.000
Max. :131.000 Max. :49.000 Max. :96.000 Max. :119.000
AFRr AMRr ASNr EURr
Min. :0.0000 Min. :0.00000 Min. :0.0000 Min. :0.0000
1st Qu.:0.0000 1st Qu.:0.00000 1st Qu.:0.0000 1st Qu.:0.0000
Median :0.5000 Median :0.04444 Median :0.0000 Median :0.0000
Mean :0.4891 Mean :0.10672 Mean :0.2113 Mean :0.1929
3rd Qu.:1.0000 3rd Qu.:0.15789 3rd Qu.:0.2941 3rd Qu.:0.3438
Max. :1.0000 Max. :1.00000 Max. :1.0000 Max. :1.0000
> summary(DenisovaMat[dene,24:31])
AFR AMR ASN EUR
Min. : 0.00 Min. : 0.000 Min. : 0.000 Min. : 0.000
1st Qu.: 2.00 1st Qu.: 0.000 1st Qu.: 0.000 1st Qu.: 0.000
Median : 10.00 Median : 1.000 Median : 0.000 Median : 0.000
Mean : 19.66 Mean : 3.521 Mean : 5.788 Mean : 5.433
3rd Qu.: 30.00 3rd Qu.: 4.000 3rd Qu.: 3.000 3rd Qu.: 3.000
Max. :157.00 Max. :49.000 Max. :101.000 Max. :110.000
AFRr AMRr ASNr EURr
Min. :0.0000 Min. :0.00000 Min. :0.0000 Min. :0.0000
1st Qu.:0.1231 1st Qu.:0.00000 1st Qu.:0.0000 1st Qu.:0.0000
Median :0.8889 Median :0.05195 Median :0.0000 Median :0.0000
Mean :0.6381 Mean :0.08716 Mean :0.1529 Mean :0.1218
3rd Qu.:0.9750 3rd Qu.:0.11628 3rd Qu.:0.1250 3rd Qu.:0.1000
Max. :1.0000 Max. :1.00000 Max. :1.0000 Max. :1.0000
>
colnames(DenisovaMat)[24]
length(which(DenisovaMat[de,24]>0))
colnames(DenisovaMat)[25]
length(which(DenisovaMat[de,25]>0))
colnames(DenisovaMat)[26]
length(which(DenisovaMat[de,26]>0))
colnames(DenisovaMat)[27]
length(which(DenisovaMat[de,27]>0))
colnames(NeanderMat)[24]
length(which(NeanderMat[ne,24]>0))
colnames(NeanderMat)[25]
length(which(NeanderMat[ne,25]>0))
colnames(NeanderMat)[26]
length(which(NeanderMat[ne,26]>0))
colnames(NeanderMat)[27]
length(which(NeanderMat[ne,27]>0))
colnames(DenisovaMat)[24]
length(which(DenisovaMat[dene,24]>0))
colnames(DenisovaMat)[25]
length(which(DenisovaMat[dene,25]>0))
colnames(DenisovaMat)[26]
length(which(DenisovaMat[dene,26]>0))
colnames(DenisovaMat)[27]
length(which(DenisovaMat[dene,27]>0))
> colnames(DenisovaMat)[24]
[1] "AFR"
> length(which(DenisovaMat[de,24]>0))
[1] 3590
> colnames(DenisovaMat)[25]
[1] "AMR"
> length(which(DenisovaMat[de,25]>0))
[1] 2390
> colnames(DenisovaMat)[26]
[1] "ASN"
> length(which(DenisovaMat[de,26]>0))
[1] 681
> colnames(DenisovaMat)[27]
[1] "EUR"
> length(which(DenisovaMat[de,27]>0))
[1] 872
c(length(which(DenisovaMat[de,24]>0)),length(which(DenisovaMat[de,25]>0)),length(which(DenisovaMat[de,26]>0)),length(which(DenisovaMat[de,27]>0)))/length(which(DenisovaMat[de,24]>0))
> c(length(which(DenisovaMat[de,24]>0)),length(which(DenisovaMat[de,25]>0)),length(which(DenisovaMat[de,26]>0)),length(which(DenisovaMat[de,27]>0)))/length(which(DenisovaMat[de,24]>0))
[1] 1.0000000 0.6657382 0.1896936 0.2428969
> colnames(NeanderMat)[24]
[1] "AFR"
> length(which(NeanderMat[ne,24]>0))
[1] 5691
> colnames(NeanderMat)[25]
[1] "AMR"
> length(which(NeanderMat[ne,25]>0))
[1] 4641
> colnames(NeanderMat)[26]
[1] "ASN"
> length(which(NeanderMat[ne,26]>0))
[1] 2867
> colnames(NeanderMat)[27]
[1] "EUR"
> length(which(NeanderMat[ne,27]>0))
[1] 3384
>
c(length(which(NeanderMat[ne,24]>0)),length(which(NeanderMat[ne,25]>0)),length(which(NeanderMat[ne,26]>0)),length(which(NeanderMat[ne,27]>0)))/length(which(NeanderMat[ne,24]>0))
> c(length(which(NeanderMat[ne,24]>0)),length(which(NeanderMat[ne,25]>0)),length(which(NeanderMat[ne,26]>0)),length(which(NeanderMat[ne,27]>0)))/length(which(NeanderMat[ne,24]>0))
[1] 1.0000000 0.8154982 0.5037779 0.5946231
> colnames(DenisovaMat)[24]
[1] "AFR"
> length(which(DenisovaMat[dene,24]>0))
[1] 4825
> colnames(DenisovaMat)[25]
[1] "AMR"
> length(which(DenisovaMat[dene,25]>0))
[1] 3677
> colnames(DenisovaMat)[26]
[1] "ASN"
> length(which(DenisovaMat[dene,26]>0))
[1] 1768
> colnames(DenisovaMat)[27]
[1] "EUR"
> length(which(DenisovaMat[dene,27]>0))
[1] 2097
c(length(which(DenisovaMat[dene,24]>0)),length(which(DenisovaMat[dene,25]>0)),length(which(DenisovaMat[dene,26]>0)),length(which(DenisovaMat[dene,27]>0)))/length(which(DenisovaMat[dene,24]>0))
> c(length(which(DenisovaMat[dene,24]>0)),length(which(DenisovaMat[dene,25]>0)),length(which(DenisovaMat[dene,26]>0)),length(which(DenisovaMat[dene,27]>0)))/length(which(DenisovaMat[dene,24]>0))
[1] 1.0000000 0.7620725 0.3664249 0.4346114
c(length(which(DenisovaMat[de,24]>0)),length(which(DenisovaMat[de,25]>0)),length(which(DenisovaMat[de,26]>0)),length(which(DenisovaMat[de,27]>0)))/length(which(DenisovaMat[de,24]>0))
c(length(which(NeanderMat[ne,24]>0)),length(which(NeanderMat[ne,25]>0)),length(which(NeanderMat[ne,26]>0)),length(which(NeanderMat[ne,27]>0)))/length(which(NeanderMat[ne,24]>0))
c(length(which(DenisovaMat[dene,24]>0)),length(which(DenisovaMat[dene,25]>0)),length(which(DenisovaMat[dene,26]>0)),length(which(DenisovaMat[dene,27]>0)))/length(which(DenisovaMat[dene,24]>0))