load(file=paste("DenisovaMat.Rda",sep="")) load(file=paste("NeanderMat.Rda",sep="")) load(file=paste("AncestMat.Rda",sep="")) load(file=paste("PopulationMat.Rda",sep="")) library(ggplot2) library(doBy) 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] de1 <- which(DenisovaMat[,12]>0.15) de2 <- which(DenisovaMat[,35]>0.3) DE1 <- which(DenisovaMat[,12]>0.3) DE2 <- which(DenisovaMat[,35]>0.6) ne1 <- which(NeanderMat[,12]>0.15) ne2 <- which(NeanderMat[,35]>0.3) NE1 <- which(NeanderMat[,12]>0.3) NE2 <- which(NeanderMat[,35]>0.6) ############################################### ## ANALYSIS length(ne) length(de) length(dene) summary(DenisovaMat[,21]) summary(DenisovaMat[,22]) summary(LLL) summary(deL) summary(neL) summary(deneL) summary(DenisovaMat[,34]) summary(NeanderMat[,34]) shorT <- which(DenisovaMat[,5]==9) shorTL <- DenisovaMat[shorT,22] summary(shorTL) 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(NeanderMat[ne,5]) summary(NeanderMat[ne,23]) summary(NeanderMat[ne,22]) summary(NeanderMat[ne,33]) summary(NeanderMat[ne,34]) summary(NeanderMat[ne,35]) 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[de,24:31]) summary(NeanderMat[ne,24:31]) summary(DenisovaMat[dene,24:31]) 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)) 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))