Description Usage Arguments Details Value See Also Examples
The core function to infer parental genotypes (MPR inference) in a local chromosome region by minimizing the number of recombination events in the population.
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baseData |
a character matrix of SNP |
allele.matrix |
a character matrix of alleles |
returnNumRecomEvents |
whether report the number of recombination events in the final result |
maxNStep |
the number of SNP in an exchange of the alleles. |
verbose |
report verbose progress. |
strEND |
the part of displaying format (verbose) |
... |
arguments to be passed to other methods. |
Several factors may affect the accuracy of MPR inference: (a). The number of SNPs processed each time (window size); (b). The density of putative SNPs (the distance between SNP sites); (c). The maximum step size of the heuristic perturbation (the parameter of maxNStep); (d). The number of RILs. And we wrote core code in C to improve computational speed.
the result of local MPR genotyping allele
NumRecomEvents,globalMPRByMarkers,globalMPRRefine,
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## select 50 SNP sites to test inference of parental genotypes from snpData.rda
data(myBaseData)
## random assignments of parental genotypes to alleles will result in
## a big number of recombinations
allele.random <- base2Allele(myBaseData)
## a big number of recombinations
NumRecomEvents(myBaseData,allele.random)
## 162
## MPR inference with maximum step size of 5
allele.MPR <- localMPR(baseData=myBaseData,maxIterate=50,maxNStep=5,showDetail=TRUE)
## should be a small number compared with random assignments above
NumRecomEvents(myBaseData,allele.MPR)
## 33
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