generateMultiHetSep: Write out multiHetSep (input of MSMC/PSMC') of simulated...
In JesseGarcia562/psmc2msprime:
Description
Usage
Arguments
Value
Examples
Description
Write out multiHetSep (input of MSMC/PSMC') of simulated individual.
Usage
1
generateMultiHetSep(msprimeVCFPath, outpath)
Arguments
outpath
Output path for the multiHetSep file that is being generated.
msprimeVCF
Path to the msprime generated VCF.
Value
Returns nothing. But writes a multihetsep (input to PSMC'/MSMC) file to the given outpath.
Examples
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msmcInference<-readMSMCInference(pathOfMSMCOutFinal = "../data/msprimeMultiHetSep/simulatedMsprime.oak.msmc.out.final.txt", mutationRate = 1e-8)
populationParametersChange<-generatePopulationParameterChanges(msmcInference)
generateMSPrimeFunction( outPath = "../code/msmc2msprime_Feb1.py", PopulationParametersChangeInput=populationParametersChange)
source_python("../code/msmc2msprime_Feb1.py")
simulation<-msmc_model(length=3e5, seed=30, mu=1.01e-08)
writeVCFOfSimulation(simulation, outpath = "../data/msprimeQLob.vcf", ploidy=2)
generateMultiHetSep(msprimeVCF = "../data/msprimeQLob.vcf",outpath = "../data/msprimeQLob_multihetsep.txt")
JesseGarcia562/psmc2msprime documentation built on May 29, 2019, 8:20 p.m.
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Description Usage Arguments Value Examples
Description
Write out multiHetSep (input of MSMC/PSMC') of simulated individual.
Usage
1 | generateMultiHetSep(msprimeVCFPath, outpath)
|
Arguments
outpath |
Output path for the multiHetSep file that is being generated. |
msprimeVCF |
Path to the msprime generated VCF. |
Value
Returns nothing. But writes a multihetsep (input to PSMC'/MSMC) file to the given outpath.
Examples
1 2 3 4 5 6 7 | msmcInference<-readMSMCInference(pathOfMSMCOutFinal = "../data/msprimeMultiHetSep/simulatedMsprime.oak.msmc.out.final.txt", mutationRate = 1e-8)
populationParametersChange<-generatePopulationParameterChanges(msmcInference)
generateMSPrimeFunction( outPath = "../code/msmc2msprime_Feb1.py", PopulationParametersChangeInput=populationParametersChange)
source_python("../code/msmc2msprime_Feb1.py")
simulation<-msmc_model(length=3e5, seed=30, mu=1.01e-08)
writeVCFOfSimulation(simulation, outpath = "../data/msprimeQLob.vcf", ploidy=2)
generateMultiHetSep(msprimeVCF = "../data/msprimeQLob.vcf",outpath = "../data/msprimeQLob_multihetsep.txt")
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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