simA noImplanted <- 1 ## how many haplotypes implanted <- 10 ## in how many samples lengthI <- 20 ## IBD length in kb simB noImplanted <- 1 ## how many haplotypes implanted <- 10 ## in how many samples lengthI <- 10 ## IBD length in kb simC noImplanted <- 1 ## how many haplotypes implanted <- 6 ## in how many samples lengthI <- 20 ## IBD length in kb simD noImplanted <- 20 ## how many haplotypes implanted <- 10 ## in how many samples lengthI <- 10 ## IBD length in kb simE noImplanted <- 5 ## how many haplotypes implanted <- 10 ## in how many samples lengthI <- 20 ## IBD length in kb PLINK! | v1.07 | 10/Aug/2009 Analysis started: Sun Feb 10 13:56:20 2013 Analysis finished: Sun Feb 10 17:28:46 2013 Germline: germline -haploid -min_m 0.001 -err_hom 0 -err_het 0 -bits 128 -bits 128 260 and 390 as filter! too many hits (30 Mio) DASH and Fabia: minsamples 5 (Dash and Fabia) Plink: pruned because of all SNVs screen -r simA a 1-25 screen -r simB a 1-25 screen -r simC a 1-25 screen -r simD a 1-25 screen -r simE a 1-25 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsA.R") screen -r simA b 26-50 screen -r simB b 26-50 screen -r simC b 26-50 screen -r simD b 26-50 screen -r simE b 26-50 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsB.R") screen -r simA c 51-75 screen -r simB c 51-75 screen -r simC c 51-75 screen -r simD c 51-75 screen -r simE c 51-75 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsC.R") screen -r simA d 76-100 screen -r simB d 76-100 screen -r simC d 76-100 screen -r simD d 76-100 screen -r simE d 76-100 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsD.R") screen -r simA plink P1 screen -r simB plink P1 screen -r simC plink P1 screen -r simD plink P1 screen -r simE plink P1 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP1.R") screen -r simA plink P2 screen -r simB plink P2 screen -r simC plink P2 screen -r simD plink P2 screen -r simE plink P2 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP2C.R") source("../compareMethodsP2.R") screen -r simA plink P3 screen -r simB plink P3 screen -r simC plink P3 screen -r simD plink P3 screen -r simE plink P3 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP3C.R") source("../compareMethodsP3.R") screen -r simA plink P4 screen -r simB plink P4 screen -r simC plink P4 screen -r simD plink P4 screen -r simE plink P4 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP4C.R") source("../compareMethodsP4.R") screen -r simA plink P23 38-50 screen -r simB plink P23 38-50 screen -r simC plink P23 38-50 screen -r simD plink P23 38-50 screen -r simE plink P23 38-50 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP23.R") screen -r simA plink P34 63-75 screen -r simB plink P34 63-75 screen -r simC plink P34 63-75 screen -r simD plink P34 63-75 screen -r simE plink P34 63-75 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP34.R") screen -r simA plink P45 88-100 screen -r simB plink P45 88-100 screen -r simC plink P45 88-100 screen -r simD plink P45 88-100 screen -r simE plink P45 88-100 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP45.R") screen -r simA plink P12 18-25 screen -r simB plink P12 18-25 screen -r simC plink P12 18-25 screen -r simD plink P12 18-25 screen -r simE plink P12 18-25 /system/apps/biosoft/R-2.14.0/bin/R source("../compareMethodsP12.R") cp ../read1000.R . /system/apps/biosoft/R-2.14.0/bin/R source("read1000.R") source("../compareMethods.R") setwd("/seppdata/sepp/linkage/Isimulation/simA") le <- c() for (i in 1:length(mergedIBD)) { le <- c(le,mergedIBD[[i]]$ibdLength) } le le1 <- c() for (i in 1:length(mergedIBD)) { poo <- mergedIBD[[i]]$snpPositions lee <- mergedIBD[[i]]$numberSnps le1 <- c(le1,(poo[lee]-poo[1])) } le1 sa <- c() for (i in 1:length(mergedIBD)) { sa <- c(sa,mergedIBD[[i]]$numberSamples) } sa sn <- c() for (i in 1:length(mergedIBD)) { sn <- c(sn,mergedIBD[[i]]$numberSnps) } sn nsa <- list() for (i in 1:length(mergedIBD)) { nsa[[i]] <- mergedIBD[[i]]$noSamples } nsa nsn <- list() for (i in 1:length(mergedIBD)) { nsn[[i]] <- mergedIBD[[i]]$noSnps } nsn ==================================================== #with standard ped/map files # --indep prunes based on the variance inflation factor (VIF), which recursively removes SNPs within a sliding window # window size in SNPs (e.g. 50), number of SNPs to shift the window at each step (e.g. 5), the VIF threshold (e.g. 2) plink_com <- paste("plink --file dataSim",run,"plink --indep-pairwise 50 5 2 --out dataSim",run,"plink",sep="") system(plink_com) # get new snp-set plink_com <- paste("plink --file dataSim",run,"plink --extract dataSim",run,"plink.prune.in --recode --out dataSim",run,"plinkpruned",sep="") system(plink_com) # --genome plink_com <- paste("plink --file dataSim",run,"plinkpruned --noweb --genome --allow-no-sex --out plink",sep="") system(plink_com) # segmental sharing plink_com <- paste("plink --file dataSim",run,"plinkpruned --noweb --read-genome plink.genome --segment --all-pairs --segment-length 0 --segment-snp 20 --out plink",run,sep="") system(plink_com) #with binary fileset # --indep prunes based on the variance inflation factor (VIF), which recursively removes SNPs within a sliding window # window size in SNPs (e.g. 50), number of SNPs to shift the window at each step (e.g. 5), the VIF threshold (e.g. 2) plink_com <- paste("plink --file dataSim",run,"plink --indep-pairwise 50 5 2 --out dataSim",run,"plink",sep="") system(plink_com) # get new snp-set and convert into binary fileset plink_com <- paste("plink --file dataSim",run,"plink --extract dataSim",run,"plink.prune.in --make-bed --out dataSim",run,"plinkpruned",sep="") system(plink_com) # --genome with binary fileset plink_com <- paste("plink --bfile dataSim",run,"plinkpruned --noweb --genome --allow-no-sex --out plink",sep="") system(plink_com) # segmental sharing with binary fileset plink_com <- paste("plink --bfile dataSim",run,"plinkpruned --noweb --read-genome plink.genome --segment --all-pairs --segment-length 0 --segment-snp 20 --out plink",run,sep="") system(plink_com) cat plinkresP1.txt plinkresP12.txt plinkresP2.txt plinkresP23.txt plinkresP3.txt plinkresP34.txt plinkresP4.txt plinkresP45.txt > plinkres.txt cat fabiaresa.txt fabiaresb.txt fabiaresc.txt fabiaresd.txt > fabiares.txt cat beagleres1a.txt beagleres1b.txt beagleres1c.txt beagleres1d.txt > beagleres1.txt cat beagleres2a.txt beagleres2b.txt beagleres2c.txt beagleres2d.txt > beagleres2.txt cat germlineres1a.txt germlineres1b.txt germlineres1c.txt germlineres1d.txt > germlineres1.txt cat germlineres2a.txt germlineres2b.txt germlineres2c.txt germlineres2d.txt > germlineres2.txt cat dashresa.txt dashresb.txt dashresc.txt dashresd.txt > dashres.txt wc ../simE/fabiares.txt wc ../simE/beagleres1.txt wc ../simE/beagleres2.txt wc ../simE/germlineres1.txt wc ../simE/germlineres2.txt wc ../simE/dashres.txt cd ./simA /system/apps/biosoft/R-2.14.0/bin/R source("../computeResult.R") q() n cd .. cd ./simB /system/apps/biosoft/R-2.14.0/bin/R source("../computeResult.R") q() n cd .. cd ./simC /system/apps/biosoft/R-2.14.0/bin/R source("../computeResult.R") q() n cd .. cd ./simD /system/apps/biosoft/R-2.14.0/bin/R source("../computeResult.R") q() n cd .. cd ./simE /system/apps/biosoft/R-2.14.0/bin/R source("../computeResult.R") q() n cd .. cd ./simA /system/apps/biosoft/R-2.14.0/bin/R source("../testSignificance.R") q() n cd .. cd ./simB /system/apps/biosoft/R-2.14.0/bin/R source("../testSignificance.R") q() n cd .. cd ./simC /system/apps/biosoft/R-2.14.0/bin/R source("../testSignificance.R") q() n cd .. cd ./simD /system/apps/biosoft/R-2.14.0/bin/R source("../testSignificance.R") q() n cd .. cd ./simE /system/apps/biosoft/R-2.14.0/bin/R source("../testSignificance.R") q() n cd ..