# Crossover analysis and genetic map construction

## Documentation for package ‘comapr’ version 1.13.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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.