Package: scoreInvHap 1.34.0

Dolors Pelegri-Siso

scoreInvHap: Get inversion status in predefined regions

scoreInvHap can get the samples' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for 21 inversions.

Authors:Carlos Ruiz [aut], Dolors Pelegrí [aut], Juan R. Gonzalez [aut, cre]

scoreInvHap_1.34.0.tar.gz
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manual.pdf |manual.html✨
card.svg |card.png
scoreInvHap/json (API)

# Install 'scoreInvHap' in R:
install.packages('scoreInvHap', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • hetRefs - Heterozygote genotypes in the references
  • info - SNP reference description
  • inversionGR - Inversions' description
  • Refs - Genotype frequency in references
  • SNPsR2 - R2 between the SNPs and the inversion status

On BioConductor:scoreInvHap-1.35.0(bioc 3.24)scoreInvHap-1.34.0(bioc 3.23)

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

snpgeneticsgenomicvariation

4.48 score 15 scripts 417 downloads 2 mentions 13 exports 70 dependencies

Last updated from:ccb6fcda81 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksERROR198
linux-devel-x86_64OK436
source / vignettesOK314
linux-release-x86_64OK417
macos-release-arm64OK285
macos-oldrel-arm64OK183
windows-develOK302
windows-releaseOK296
windows-oldrelOK318
wasm-releaseOK155

Exports:certaintycheckSNPsclassificationclassifSNPsclassifSNPsImputediffscoresmaxscoresnumSNPsplotCallRateplotScorespropSNPsscoreInvHapscores

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowsnpStatsSparseArraySummarizedExperimentsurvivalsysVariantAnnotationvctrsXMLXVectoryaml

Inversion genotyping with scoreInvHap

Carlos Ruiz-Arenas, Alejandro Caceres, Juan R. Gonzalez

Rendered fromscoreInvHap.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-06-07
Started: 2017-06-22

Readme and manuals

Help Manual

Help pageTopics
Adapt references to imputed dataadaptRefs
Check genotype objectcheckSNPs
Get similarity scores and probabilityclassifSNPs classifSNPsImpute
Compute all similarity scores for a samplecomputeScore
Solve genotypes discrepanciescorrectAlleleTable
Compute the allele tablegetAlleleTable
Get genotypes tablegetGenotypesTable
Get the inversion status of a samplegetInvStatus
Heterozygote genotypes in the referenceshetRefs
SNP reference descriptioninfo
Inversions' descriptioninversionGR
Modify feature data from VCFprepareMap
Genotype frequency in referencesRefs
scoreInvHap: package to get inversion status of predefined regions.scoreInvHap
scoreInvHapRes instancescertainty certainty,scoreInvHapRes-method classification classification,scoreInvHapRes-method diffscores diffscores,scoreInvHapRes-method maxscores maxscores,scoreInvHapRes-method numSNPs numSNPs,scoreInvHapRes-method plotCallRate plotCallRate,scoreInvHapRes-method plotScores plotScores,scoreInvHapRes-method propSNPs propSNPs,scoreInvHapRes-method scoreInvHapRes scoreInvHapRes-class scoreInvHapRes-methods scores scores,scoreInvHapRes-method
R2 between the SNPs and the inversion statusSNPsR2