1000G_ancient_per_population.R: Calculates the number of Neandertal- and Denisovan-matching IBD segments shared exclusively by a particular continental population for each chromosome and the number of Neandertal- and Denisovan-matching IBD segments shared exclusively by Africans that are observed in a particular subpopulation ########################################################################################## 1000G_plotLength_chr.R: Plots histograms of length of IBD segments on chromosome X and densities of lengths of IBD segments on chromosome X that match the Neandertal or Denisovan genome and are shared by a particular population or groups of populations ########################################################################################## 1000G_plotLength_G.R: Plots histograms of length of IBD segments on the autosomes and densities of lengths of IBD segments on the autosomes that match the Neandertal or Denisovan genome and are shared by a particular population or groups of populations ########################################################################################## 1000G_plotMajPie_chr.R: Plots pie charts for chromosome X reflecting the different genomes and by the color the population to which more than 50% of the individuals with the corresponding IBD segment belong ########################################################################################## 1000G_plotMajPie_G.R: Plots pie charts for the autosomes reflecting the different genomes and by the color the population to which more than 50% of the individuals with the corresponding IBD segment belong ########################################################################################## 1000G_pop_functions.R: Extracts IBD segments from PopulationMat and SubPopMat that are shared / not shared by a certain fraction of individuals from a certain population ########################################################################################## The fields of DenisovaMat, NeanderMat: [1] "allCount1" "allCount" "ibdC" "posAll" [5] "#SNVsOrig" "#SNVs" "#Nea" "#Ref" [9] "#Alt" "#New" "NeaR" "RefR" [13] "AltR" "NewR" "xAltCon" "xRefCon" [17] "mAltCon" "mRefCon" "NeaPosC" "AltPosC" [21] "RefPosC" "IBDlength" "IBDlengthCorrected" "#samples" [25] "AFR" "AMR" "EAS" "EUR" [29] "SAS" "AFRr" "AMRr" "EASr" [33] "EURr" "SASr" "ancientLengthSNVs" "ancientLength" [37] "ancientRatio" "allCount1" non redundant IBD segment count "allCount" count with redundant IBD segments "ibdC" Number of IBD segments in this interval "posAll" Number of the current interval "#SNVsOrig" Number of tagSNVs "#SNVs" Number of tagSNVs in IBD segment with corrected length "#Nea" Number of SNVs called in ancient 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 ancient 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 (ancient-human) pos. (minor hum) "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 "EAS" number of East Asians "EUR" number of Europeans "SAS" number of South Asians "AFRr" ratio of Africans "AMRr" ratio of admixed Americans "EASr" ratio of East Asians "EURr" ratio of Europeans "SASr" ratio of South Asians "ancientLengthSNVs" number of tagSNVs in ancient part - 1 (note the -1 !) "ancientLength" length of ancient part "ancientRatio" ratio of matching tagSNVs in ancient part NOTE: ancient refers always to the genome that is indicated by the filename ########################################################################################## The fields of AncDenisovaMat, AncNeanderMat: [1] "allCount1" "allCount" "ibdC" "posAll" [5] "#SNPs" "#Nea" "#Ref" "#Alt" [9] "#New" "NeaR" "RefR" "AltR" [13] "NewR" "xAltCon" "xRefCon" "mAltCon" [17] "mRefCon" "NeaPosC" "AltPosC" "RefPosC" [21] "IBDlength" "IBDlengthCorrected" "#samples" "AFR" [25] "AMR" "EAS" "EUR" "SAS" [29] "AFRr" "AMRr" "EASr" "EURr" [33] "SASr" "IBDlengthNew" "ancientLengthSNVs" "ancientLength" [37] "ancientRatio" "ancestorSNPs" "ancestorRatio" [1] - [37] see DenisovaMat, NeanderMat "ancestorSNPs" number of tagSNVs in ancient part matching the ancestral sequence "ancestorRatio" ratio of tagSNVs in ancient part matching the ancestral sequence ########################################################################################## The fields of PopulationMat: [1] "allCount1" "allCount" "ibdC" "posAll" "#Samples" "AFR" "AMR" "EAS" [9] "EUR" "SAS" "allCount1" non redundant IBD segment count "allCount" count with redundant IBD segments "ibdC" number of IBD segments in this interval "posAll" number of the current interval "#Samples" number of samples with this IBD segment "AFR" ratio of Africans "AMR" ratio of admixed Americans "EAS" ratio of East Asians "EUR" ratio of Europeans "SAS" ratio of South Asians ########################################################################################## The fields of SubPopulationMat: [1] "allCount1" "allCount" "ibdC" "posAll" "#Samples" "ACB" "ASW" "BEB" "CDX" "CEU" [11] "CHB" "CHS" "CLM" "ESN" "FIN" "GBR" "GIH" "GWD" "IBS" "ITU" [21] "JPT" "KHV" "LWK" "MSL" "MXL" "PEL" "PJL" "PUR" "STU" "TSI" [31] "YRI" "ACBr" "ASWr" "BEBr" "CDXr" "CEUr" "CHBr" "CHSr" "CLMr" "ESNr" [41] "FINr" "GBRr" "GIHr" "GWDr" "IBSr" "ITUr" "JPTr" "KHVr" "LWKr" "MSLr" [51] "MXLr" "PELr" "PJLr" "PURr" "STUr" "TSIr" "YRIr" "allCount1" non redundant IBD segment count "allCount" count with redundant IBD segments "ibdC" number of IBD segments in this interval "posAll" number of the current interval "#Samples" number of samples with this IBD segment "ACB" number of African Caribbeans in Barbados "ASW" number of Americans with African ancestry from SW US ... "YRI" number of Yoruba in Ibadan, Nigeria "ACBr" ratio of African Caribbeans in Barbados "ASWr" ratio of Americans with African ancestry from SW US ... "YRIr" ratio of Yoruba in Ibadan, Nigeria ########################################################################################## ibdMat: sparse matrix with individuals as rows and IBD segments as columns. 1 in row i and column j indicates that individual i shares IBD segment j ########################################################################################## GRanges_chrn.Rda: GRanges object of all IBD segments of a certain chromosome metacolumns identify the IBD segment: "allCount1" non redundant IBD segment count "ibdC" number of IBD segments in this interval "posAll" number of the current interval