simulateIBDsegments
: R implementation of simulateIBDsegments
.
Genotype data with rare variants is simulated. Into these datan IBD segments are implanted. All data sets and information are written to files.
simulateIBDsegments(fileprefix="dataSim",minruns=1, maxruns=100,snvs=10000,individualsN=100,avDistSnvs=100, avDistMinor=25,noImplanted=1,implanted=10,length=100, minors=20,mismatches=0,mismatchImplanted=0.5,overlap=50, noOverwrite=FALSE)
1/avDistMinor
is the average minor allele frequency (MAF).noOverwrite=TRUE
ensures that an IBD segment is not superimposed by another IBD segment.Data simulations focuses on rare variants but common variants are possible, too. Linkage disequilibrium and haplotype blocks are not simulated except by implanting IBD segments.
Simulated data is written to files. For BEAGLE the data is written to "...beagle.txt". For PLINK the data is written to "...plink.ped", "...plink.map", and "...plink.fam". For the MCMC method the data is written to "...mcmc.genotype", "...mcmc.posmaf", and "...mcmc.initz". For RELATE the data is written to "...relate.geno", "...relate.pos", and "...relate.chr". For fabia the data is written to "...fabia_individuals.txt", "...fabia_annot.txt" "...fabia_mat.txt".
Information on parameters for data simulation is written to "...Parameters.txt" while information on implanted IBD segments is written to "...Impl.txt".
Most information is also written in R binary ".Rda" files.
Implementation in R.
S. Hochreiter et al., FABIA: Factor Analysis for Bicluster Acquisition, Bioinformatics 26(12):1520-1527, 2010.
IBDsegment-class
,
IBDsegmentList-class
,
analyzeIBDsegments
,
compareIBDsegmentLists
,
extractIBDsegments
,
findDenseRegions
,
hapFabia
,
hapFabiaVersion
,
hapRes
,
chr1ASW1000G
,
IBDsegmentList2excel
,
identifyDuplicates
,
iterateIntervals
,
makePipelineFile
,
matrixPlot
,
mergeIBDsegmentLists
,
mergedIBDsegmentList
,
plotIBDsegment
,
res
,
setAnnotation
,
setStatistics
,
sim
,
simu
,
simulateIBDsegmentsFabia
,
simulateIBDsegments
,
split_sparse_matrix
,
toolsFactorizationClass
,
vcftoFABIA
## Not run:
# old_dir <- getwd()
# setwd(tempdir())
#
# simulateIBDsegments(minruns=1,maxruns=1,snvs=1000,individualsN=10,avDistSnvs=100,avDistMinor=15,noImplanted=1,implanted=10,length=100,minors=10,mismatches=0,mismatchImplanted=0.5,overlap=50,noOverwrite=FALSE)
#
# setwd(old_dir)
#
# ## End(Not run)
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