R: Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

# Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells

## Documentation for package ‘Hapi’ version 0.0.3

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

## Help Pages

Hapi-package | Hapi is a novel easy-to-use package that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and next generation sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of crossovers in the gametes.
base2num | Convert genotype coded in A/T/C/G to 0/1
crossover | Crossover information across all gamete cells
gamete11 | Haplotypes of a single gamete cell for visualization
gmt | Raw genotyping data
Hapi | Hapi is a novel easy-to-use package that only requires 3 to 5 gametes to reconstruct accurate and high-resolution haplotypes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and next generation sequencing even with low-coverage. Hapi simply takes genotype data of known hetSNPs in single gamete cells as input and report the high-resolution haplotypes as well as confidence level of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of crossovers in the gametes.
hapiAssemble | Consensus haplotype assembly
hapiAssembleEnd | Assembly of haplotypes in regions at the end of a chromosome
hapiAutoPhase | Automatic inference of haplotypes
hapiBlockMPR | Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypes
hapiCVCluster | Filter out hetSNPs in potential complex regions
hapiCVDistance | Histogram of crossover distance
hapiCVMap | Visualization of crossover map
hapiCVResolution | Histogram of crossover resolution
hapiFilterError | Filter out hetSNPs with potential genotyping errors
hapiFrameSelection | Selection of hetSNPs to form a framework
hapiGameteView | Visualization of haplotypes in a single gamete cell
hapiIdentifyCV | Indentify crossovers in gamete cells
hapiImupte | Imputation of missing genotypes in the framework
hapiPhase | Phase draft haplotypes by majority voting
hg19 | Chromosome information of hg19
num2base | Convert genotype coded in 0/1 to A/T/C/G