Package: GHap 4.0.0.12

GHap: Genome-Wide Haplotyping

Haplotype calling from phased marker data. Given user-defined haplotype blocks (HapBlock), the package identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes (HapGenotype) based on HapAllele dose (i.e. 0, 1 or 2 copies). The output is not only useful for analyses that can handle multi-allelic markers, but is also conveniently formatted for existing pipelines intended for bi-allelic markers. The package was first described in Bioinformatics by Utsunomiya et al. (2016, <doi:10.1093/bioinformatics/btw356>). Since the v2 release, the package provides functions for unsupervised and supervised detection of ancestry tracks. The methods implemented in these functions were described in an article published in Methods in Ecology and Evolution by Utsunomiya et al. (2020, <doi:10.1111/2041-210X.13467>). The source code for v3 was modified for improved performance and inclusion of new functionality, including analysis of unphased data, runs of homozygosity, sampling methods for virtual gamete mating, mixed model fitting and GWAS.

Authors:Yuri Tani Utsunomiya

GHap_4.0.0.12.tar.gz

GHap_4.0.0.12.tgz(r-4.4-x86_64)GHap_4.0.0.12.tgz(r-4.4-arm64)GHap_4.0.0.12.tgz(r-4.3-x86_64)GHap_4.0.0.12.tgz(r-4.3-arm64)
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GHap.pdf |GHap.html
GHap/json (API)

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

Peer review:

Bug tracker:https://github.com/ytutsunomiya/ghap/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

6.74 score 5 stars 44 scripts 249 downloads 10 mentions 45 exports 19 dependencies

Last updated 1 months agofrom:65575819d4. Checks:OK: 1 WARNING: 5. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 10 2024
R-4.5-linux-x86_64WARNINGNov 10 2024
R-4.4-mac-x86_64WARNINGNov 10 2024
R-4.4-mac-aarch64WARNINGNov 10 2024
R-4.3-mac-x86_64WARNINGNov 10 2024
R-4.3-mac-aarch64WARNINGNov 10 2024

Exports:ghap.anc2plinkghap.ancmarkghap.ancplotghap.ancsmoothghap.ancsvmghap.anctestghap.anctrainghap.assocghap.blockgenghap.blockstatsghap.compressghap.exfilesghap.fast2phaseghap.freqghap.frohghap.fstghap.getHinvghap.hap2plinkghap.haplotypingghap.hapstatsghap.ibdghap.inbcoefghap.karyoplotghap.kinshipghap.lmmghap.loadhaploghap.loadphaseghap.loadplinkghap.makefileghap.manhattanghap.oxford2phaseghap.pedcheckghap.phase2plinkghap.predictblupghap.profileghap.relfindghap.remlcighap.rohghap.simadmixghap.simmatingghap.simphenoghap.sliceghap.subsetghap.varblupghap.vcf2phase

Dependencies:bootclassdata.tabledotCall64e1071latticelme4MASSMatrixminqanlmenloptrpedigreemmproxyRcppRcppEigenspamsparseinvstringi

GHap vignette

Rendered fromGHap_vignette.pdf.asisusingR.rsp::asison Nov 10 2024.

Last update: 2021-04-23
Started: 2021-04-23

Readme and manuals

Help Manual

Help pageTopics
Convert ancestry tracks to PLINK binaryghap.anc2plink
Per marker ancestry proportionsghap.ancmark
Barplot of predictions of ancestry proportionsghap.ancplot
Smoothing of haplotype ancestry predictionsghap.ancsmooth
SVM-based predictions of haplotype ancestryghap.ancsvm
Prediction of haplotype ancestryghap.anctest
Construction of prototype allelesghap.anctrain
Genome-wide association analysisghap.assoc
Haplotype block generatorghap.blockgen
HapBlock statisticsghap.blockstats
Compress phased genotype dataghap.compress
Example filesghap.exfiles
Convert fastPHASE data into the GHap phase formatghap.fast2phase
Compute marker allele frequenciesghap.freq
Calculation of genomic inbreeding (FROH)ghap.froh
Haplotype-based Fstghap.fst
Compute the inverse of Hghap.getHinv
Convert haplotype allele counts to PLINK binaryghap.hap2plink
Haplotype genotypesghap.haplotyping
Haplotype allele statisticsghap.hapstats
Estimation of IBD sharingghap.ibd
Compute measures of inbreedingghap.inbcoef
Individual chromosome paintingghap.karyoplot
Relationship matrix based on genomic dataghap.kinship
Linear mixed modelghap.lmm
Load haplotype genotype dataghap.loadhaplo
Load binary phased genotype dataghap.loadphase
Load binary PLINK dataghap.loadplink
Create example input filesghap.makefile
Manhattan plotghap.manhattan
Convert Oxford data into GHap phaseghap.oxford2phase
Summary statistics for pedigreeghap.pedcheck
Export phase object to PLINK binaryghap.phase2plink
Predict BLUP from referenceghap.predictblup
Genomic profileghap.profile
Find relatives in IBD estimatesghap.relfind
Confidence intervals for functions of variance componentsghap.remlci
Detection of runs of homozygosity (ROH)ghap.roh
Simulate individuals from specified admixture proportionsghap.simadmix
Simulate individuals from specified matingsghap.simmating
Quantitative trait simulation using real genotype dataghap.simpheno
Get a slice of a GHap objectghap.slice
Subset GHap objectsghap.subset
Convert BLUP of individuals into BLUP of variantsghap.varblup
Convert VCF data into GHap phaseghap.vcf2phase