Crossover analysis and genetic map construction


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Documentation for package ‘comapr’ version 1.10.0

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bootstrapDist bootstrapDist
calGeneticDist calGeneticDist
calGeneticDist-method calGeneticDist
coCount RangedSummarizedExperiment object containing the crossover counts across samples for the list of SNP marker intervals
comapr 'comapr' package
combineHapState combineHapState
correctGT correctGT
countBinState countBinState
countCOs countCOs
countCOs-method countCOs
countGT countGT
filterGT filterGT
filterGT-method filterGT
findDupSamples findDupSamples
getAFTracks getAFTracks
getCellAFTrack getCellAFTrack Generates the DataTracks for plotting AF and crossover regions
getCellCORange getCellCORange
getCellDPTrack getCellDPTrack Generates the DataTrack for plotting DP of a selected cell
getDistortedMarkers getDistortedMarkers
getMeanDPTrack getMeanDPTrack
getSNPDensityTrack getSNPDensityTrack
parents_geno Parents' genotype for F1 samples in 'snp_geno'
perCellChrQC perCellChrQC
permuteDist permuteDist
perSegChrQC perSegChrQC
plotCount plotCount
plotCount-method plotCount
plotGeneticDist plotGeneticDist
plotGTFreq plotGTFreq
plotWholeGenome Plot cumulative genetic distances across the genome
readColMM readColMM
readHapState readHapState
snp_geno Markers by genotype results for a group of samples
snp_geno_gr Markers by genotype results for a group of samples
twoSamples RangedSummarizedExperiment object containing the Viterbi states SNP markers for samples from two groups. 'colData(twoSamples)' contains the sample group factor.