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

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Documentation for package ‘Hapi’ version 0.0.3

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

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