old_dir <- getwd()
setwd(tempdir())
data(simu)
namesL <- simu[["namesL"]]
haploN <- simu[["haploN"]]
snvs <- simu[["snvs"]]
annot <- simu[["annot"]]
alleleIimp <- simu[["alleleIimp"]]
write.table(namesL,file="dataSim1fabia_individuals.txt",
quote = FALSE,row.names = FALSE,col.names = FALSE)
write(as.integer(haploN),file="dataSim1fabia_annot.txt",
ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_annot.txt",
append=TRUE,ncolumns=100)
write.table(annot,file="dataSim1fabia_annot.txt",
sep = " ",quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write(as.integer(haploN),file="dataSim1fabia_mat.txt",
ncolumns=100)
write(as.integer(snvs),file="dataSim1fabia_mat.txt",
append=TRUE,ncolumns=100)
for (i in 1:haploN) {
a1 <- which(alleleIimp[i,]>0.01)
al <- length(a1)
b1 <- alleleIimp[i,a1]
a1 <- a1 - 1
dim(a1) <- c(1,al)
b1 <- format(as.double(b1),nsmall=1)
dim(b1) <- c(1,al)
write.table(al,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write.table(a1,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
write.table(b1,file="dataSim1fabia_mat.txt",
sep = " ", quote = FALSE,row.names = FALSE,
col.names = FALSE,append=TRUE)
}
hapRes <- hapFabia(fileName="dataSim1fabia",prefixPath="",
sparseMatrixPostfix="_mat",
annotPostfix="_annot.txt",individualsPostfix="_individuals.txt",
labelsA=NULL,pRange="",individuals=0,lowerBP=0,upperBP=0.15,
p=10,iter=1,quant=0.01,eps=1e-5,alpha=0.03,cyc=50,non_negative=1,
write_file=0,norm=0,lap=100.0,IBDsegmentLength=10,Lt = 0.1,
Zt = 0.2,thresCount=1e-5,mintagSNVsFactor=3/4,pMAF=0.1,
haplotypes=FALSE,cut=0.8,procMinIndivids=0.1,thresPrune=1e-3,
simv="minD",minTagSNVs=6,minIndivid=2,avSNVsDist=100,SNVclusterLength=100)
summary(hapRes$mergedIBDsegmentList)
plot(hapRes$mergedIBDsegmentList[[1]],filename="dataSim1fabia_mat")
### Another Example
simulateIBDsegmentsFabia(fileprefix="dataSim",
minruns=2,maxruns=2,snvs=1000,individualsN=100,
avDistSnvs=100,avDistMinor=10,noImplanted=1,
implanted=10,length=50,minors=30,mismatches=0,
mismatchImplanted=0.5,overlap=50)
hapRes <- hapFabia(fileName="dataSim2fabia",prefixPath="",
sparseMatrixPostfix="_mat",
annotPostfix="_annot.txt",individualsPostfix="_individuals.txt",
labelsA=NULL,pRange="",individuals=0,lowerBP=0,upperBP=0.15,
p=10,iter=1,quant=0.01,eps=1e-5,alpha=0.03,cyc=50,non_negative=1,
write_file=0,norm=0,lap=100.0,IBDsegmentLength=10,Lt = 0.1,
Zt = 0.2,thresCount=1e-5,mintagSNVsFactor=3/4,pMAF=0.1,
haplotypes=FALSE,cut=0.8,procMinIndivids=0.1,thresPrune=1e-3,
simv="minD",minTagSNVs=6,minIndivid=2,avSNVsDist=100,SNVclusterLength=100)
## Summary of the IBD segment list
summary(hapRes$mergedIBDsegmentList)
## Summary of the IBD segment
summary(hapRes$mergedIBDsegmentList[[1]])
## Plot an IBD segment
plot(hapRes$mergedIBDsegmentList[[1]],filename="dataSim2fabia_mat")
## Not run:
# ## It is interactive, thus dontrun!
#
# ## Plot an IBD segment list
# plot(hapRes$mergedIBDsegmentList,filename="dataSim2fabia_mat")
#
# ## End(Not run)
setwd(old_dir)
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