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| | ;THIS PAGE IS OBSOLETE, PLEASE SEE FST AND PCA in the sidebar for the latest versions |
| Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files. | | Matteo Fumagalli has been working on methods to estimate Fst and doing PCA/Covariance based on ANGSD output files. |
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| The main documentation for this is found here: | | The main documentation for this is found here: |
| https://github.com/mfumagalli/ngsTools | | https://github.com/mfumagalli/ngsTools |
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| For the new fancy fst estimation, you should use the latests github version.
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| =Fst= | | =Fst= |
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| =cite= | | =cite= |
| If you use these methods, you should cite the m. fumagalli paper http://www.ncbi.nlm.nih.gov/pubmed/23979584 | | If you use these methods, you should cite the m. fumagalli paper http://www.ncbi.nlm.nih.gov/pubmed/23979584 |
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| =New Fancy Method (sim data)=
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| <pre>
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| nRep <- 100
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| nPop1 <- 24
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| nPop2 <- 16
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| cmd <- paste("msms -ms",nPop1+nPop2,nRep,"-t 930 -r 400 -I 2",nPop1,nPop2,"0 -g 1 9.70406 -n 1 2 -n 2 1 -ma x 0.0 0.0 x -ej 0.07142857 2 1 >msoutput.txt ",sep=" ")
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| system(cmd)
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| ##system("msms -ms 40 1 -t 930 -r 400 -I 2 20 20 0 -g 1 9.70406 -n 1 2 -n 2 1 -ma x 0.0 0.0 x -ej 0.07142857 2 1 >msoutput.txt ")
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| source("../R/readms.output.R")
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| to2dSFS <- function(p1.d,p2.d,nPop1,nPop2)
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| sapply(0:nPop1,function(x) table(factor(p2.d[p1.d==x],levels=0:nPop2)))
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| source("../R/readms.output.R")
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| a<- read.ms.output(file="msoutput.txt")
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| p1.d <- unlist((sapply(a$gam,function(x) colSums(x[1:nPop1,]))))
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| p2.d <- unlist((sapply(a$gam,function(x) colSums(x[-c(1:nPop1),]))))
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| par(mfrow=c(1,2))
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| barplot(table(p1.d))
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| barplot(table(p2.d))
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| sfs.2d <- t(sapply(0:nPop1,function(x) table(factor(p2.d[p1.d==x],levels=0:nPop2))))
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| system("../misc/msToGlf -in msoutput.txt -out raw -singleOut 1 -regLen 0 -depth 8 -err 0.005")
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| system("../misc/splitgl raw.glf.gz 20 1 12 >pop1.glf.gz")
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| system("../misc/splitgl raw.glf.gz 20 13 20 >pop2.glf.gz")
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| system("echo \"1 250000000\" >fai.fai")
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| system("../angsd -glf pop1.glf.gz -nind 12 -doSaf 1 -out pop1 -fai fai.fai -issim 1")
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| system("../angsd -glf pop2.glf.gz -nind 8 -doSaf 1 -out pop2 -fai fai.fai -issim 1")
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| system("../misc/realSFS pop1.saf.idx >pop1.saf.idx.ml")
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| system("../misc/realSFS pop2.saf.idx >pop2.saf.idx.ml")
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| system("../misc/realSFS pop1.saf.idx pop2.saf.idx -maxIter 500 -p 20 >pop1.pop2.saf.idx.ml")
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| getFst<-function(est){
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| N1<-nrow(est)-1
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| N2<-ncol(est)-1
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| cat("N1: ",N1 ," N2: ",N2,"\n")
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| est0<-est
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| est0[1,1]<-0
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| est0[N1+1,N2+1]<-0
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| est0<-est0/sum(est0)
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| aMat<<-matrix(NA,nrow=N1+1,ncol=N2+1)
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| baMat<<-matrix(NA,nrow=N1+1,ncol=N2+1)
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| for(a1 in 0:(N1))
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| for(a2 in 0:(N2)){
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| p1 <- a1/N1
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| p2 <- a2/N2
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| q1 <- 1 - p1
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| q2 <- 1 - p2
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| alpha1 <- 1 - (p1^2 + q1^2)
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| alpha2 <- 1 - (p2^2 + q2^2)
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| al <- 1/2 * ( (p1-p2)^2 + (q1-q2)^2) - (N1+N2) * (N1*alpha1 + N2*alpha2) / (4*N1*N2*(N1+N2-1))
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| bal <- 1/2 * ( (p1-p2)^2 + (q1-q2)^2) + (4*N1*N2-N1-N2)*(N1*alpha1 + N2*alpha2) / (4*N1*N2*(N1+N2-1))
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| aMat[a1+1,a2+1]<<-al
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| baMat[a1+1,a2+1]<<-bal
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| ## print(signif(c(a1=a1,a2=a2,p1=p1,p2=p2,al1=alpha1,al2=alpha2,al),2))
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| }
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| ## unweighted average of single-locus ratio estimators
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| fstU <- sum(est0*(aMat/baMat),na.rm=T)
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| ## weighted average of single-locus ratio estimators
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| fstW <- sum(est0*aMat,na.rm=T)/sum(est0*baMat,na.rm=T)
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| c(fstW=fstW,fstU=fstU)
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| }
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| > getFst(sfs.2d)
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| N1: 24 N2: 16
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| fstW fstU
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| 0.11945801 0.08249571
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| est <- matrix(as.integer(scan("pop1.pop2.saf.idx.ml")),byrow=T,ncol=nPop2+1)
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| > getFst(est)
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| N1: 24 N2: 16
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| fstW fstU
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| 0.11925903 0.08241461
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| cmd<"fst index pop1.saf.idx pop2.saf.idx -sfs pop1.pop2.saf.idx.ml -fstout testing"
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| system(cmd)
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|
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| ##view the per site 'alpha' 'beta' if you want
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| cmd<-"../misc/realSFS fst print testing.fst.idx |head"
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|
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| ##use fancy new emperical bayes
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| cmd<- "../misc/realSFS fst stats testing.fst.idx "
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| system(cmd)
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| -> FST.Unweight:0.083316 Fst.Weight:0.119372
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| </pre>
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| =new fancy version=
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| <pre>
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| #this is with 2pops
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| ../angsd -b list1 -anc hg19ancNoChr.fa -out pop1 -dosaf 1 -gl 1
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| ../angsd -b list2 -anc hg19ancNoChr.fa -out pop1 -dosaf 1 -gl 1
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| ../misc/realSFS pop1.saf.idx pop2.saf.idx >pop1.pop2.ml
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| ../misc/realSFS fst index pop1.saf.idx pop2.saf.idx -sfs pop1.pop2.ml -fstout here
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| ../misc/realSFS fst stats here.fst.idx
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| -> FST.Unweight:0.069395 Fst.Weight:0.042349
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| =3pops=
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| <pre>
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| msms -ms 41 10 -t 930 -r 400 -I 3 11 13 17 -n 1 1.682020 -n 2 3.736830 -n 3 7.292050 -eg 0 2 116.010723 -eg 0 3 160.246047 -ma x 0.881098 0.561966 0.881098 x 2.797460 0.561966 2.797460 x -ej 0.028985 3 2 -en 0.028985 2 0.287184 -ema 0.028985 3 x 7.293140 x 7.293140 x x x x x -ej 0.197963 2 1 -en 0.303501 1 1
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| </pre>
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