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| MPR.genotyping-package | Maximum Parsimony of Recombination to Infer Parental Genotypes |
| base2Allele | Get Initial Allele from SNP Matrix |
| base2Geno | Formatting the Matrix of SNP to Int Type |
| base2Geno_ori | Formatting the Matrix of SNP to Int Type(NA) |
| checkData | Data for check |
| correctFUNHMM | correct FUN HMM |
| correctGeno | Correct Geno |
| findBlockAndFilter | find Block And Filter |
| fSNP | Example data of negative SNP |
| geno2Cross | geno to Cross |
| genoToBin | geno To Bin |
| genotypeCallsBayes | genotype Calls by Bayes |
| globalMPRByMarkers | MPR inference in whole chromosome |
| globalMPRRefine | refine SNPs by resampling |
| globalMPRwithoutMarkers | MPR without Markers |
| hmm.vitFUN.rils | Genotyping by HMM |
| localMPR | infer parental genotypes by minimizing the number of recombination events |
| makeEmissionFUN | emission of HMM |
| markerData | Data of Markers |
| mergeBinMap | merge Bin Map |
| mergeBlocks | merge Blocks |
| MPR.genotyping | Maximum Parsimony of Recombination to Infer Parental Genotypes |
| myBaseData | Example SNP data(smaller) |
| NumRecomEvents | calculate the number of recombination events |
| phenoData | data of phenotype |
| phy2get.haldane.rils | transition of HMM |
| snpData | Example SNP data |