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MPR.genotyping (version 0.8)

Maximum Parsimony of Recombination to Infer Parental Genotypes

Description

Infer parental genotypes based on low-coverage population sequencing data and thus can genotype mapping populations and construct ultra-high density linkage map in a parent-independent manner. Weibo Xie et al. (2010) .

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Version

Install

install.packages('MPR.genotyping')

Monthly Downloads

5

Version

0.8

License

GPL (>= 2)

Maintainer

Weitong Guo

Last Published

January 24th, 2018

Functions in MPR.genotyping (0.8)

correctFUNHMM

correct FUN HMM
correctGeno

Correct Geno
base2Geno_ori

Formatting the Matrix of SNP to Int Type(NA)
checkData

Data for check
geno2Cross

geno to Cross
genoToBin

geno To Bin
mergeBinMap

merge Bin Map
mergeBlocks

merge Blocks
findBlockAndFilter

find Block And Filter
globalMPRRefine

refine SNPs by resampling
globalMPRwithoutMarkers

MPR without Markers
fSNP

Example data of negative SNP
hmm.vitFUN.rils

Genotyping by HMM
localMPR

infer parental genotypes by minimizing the number of recombination events
myBaseData

Example SNP data(smaller)
phenoData

data of phenotype
MPR.genotyping-package

MPR.genotyping
NumRecomEvents

calculate the number of recombination events
makeEmissionFUN

emission of HMM
markerData

Data of Markers
phy2get.haldane.rils

transition of HMM
snpData

Example SNP data
base2Allele

Get Initial Allele from SNP Matrix
base2Geno

Formatting the Matrix of SNP to Int Type
genotypeCallsBayes

genotype Calls by Bayes
globalMPRByMarkers

MPR inference in whole chromosome