Package: Hapi 0.0.3

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

Inference of chromosome-length haplotypes using a few haploid gametes of an individual. The gamete genotype data may be generated from various platforms including genotyping arrays and 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 of each phased hetSNPs. The package also includes a module allowing downstream analyses and visualization of identified crossovers in the gametes.

Authors:Ruidong Li, Han Qu, Jinfeng Chen, Shibo Wang, Le Zhang, Julong Wei, Sergio Pietro Ferrante, Mikeal L. Roose, Zhenyu Jia

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Hapi.pdf |Hapi.html✨
Hapi/json (API)
NEWS

# Install 'Hapi' in R:
install.packages('Hapi', repos = c('https://rli012.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • crossover - Crossover information across all gamete cells
  • gamete11 - Haplotypes of a single gamete cell for visualization
  • gmt - Raw genotyping data
  • hg19 - Chromosome information of hg19

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

snpgenomicvariationgeneticshiddenmarkovmodelsinglecellsequencingmicroarray

3.79 score 41 scripts 124 downloads 3 mentions 16 exports 29 dependencies

Last updated 6 years agofrom:6cd2fcf8cf. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 03 2024
R-4.5-winOKNov 03 2024
R-4.5-linuxOKNov 03 2024
R-4.4-winOKNov 03 2024
R-4.4-macOKNov 03 2024
R-4.3-winOKNov 03 2024
R-4.3-macOKNov 03 2024

Exports:base2numhapiAssemblehapiAssembleEndhapiAutoPhasehapiBlockMPRhapiCVClusterhapiCVDistancehapiCVMaphapiCVResolutionhapiFilterErrorhapiFrameSelectionhapiGameteViewhapiIdentifyCVhapiImuptehapiPhasenum2base

Dependencies:clicolorspacefansifarverggplot2gluegtableHMMisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Hapi: an R package for chromosome-length haplotype inference using genotypic data of single gamete cells

Ruidong Li and Zhenyu Jia Department of Plant and Botany Sciences, Univeristy of California, Riverside

Rendered fromHapi.Rmdusingknitr::rmarkdownon Nov 03 2024.

Last update: 2018-07-28
Started: 2018-07-28

Readme and manuals

Help Manual

Help pageTopics
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.Hapi-package Hapi
Convert genotype coded in A/T/C/G to 0/1base2num
Crossover information across all gamete cellscrossover
Haplotypes of a single gamete cell for visualizationgamete11
Raw genotyping datagmt
Consensus haplotype assemblyhapiAssemble
Assembly of haplotypes in regions at the end of a chromosomehapiAssembleEnd
Automatic inference of haplotypeshapiAutoPhase
Maximum Parsimony of Recombination (MPR) for proofreading of draft haplotypeshapiBlockMPR
Filter out hetSNPs in potential complex regionshapiCVCluster
Histogram of crossover distancehapiCVDistance
Visualization of crossover maphapiCVMap
Histogram of crossover resolutionhapiCVResolution
Filter out hetSNPs with potential genotyping errorshapiFilterError
Selection of hetSNPs to form a frameworkhapiFrameSelection
Visualization of haplotypes in a single gamete cellhapiGameteView
Indentify crossovers in gamete cellshapiIdentifyCV
Imputation of missing genotypes in the frameworkhapiImupte
Phase draft haplotypes by majority votinghapiPhase
Chromosome information of hg19hg19
Convert genotype coded in 0/1 to A/T/C/Gnum2base