Package: scoreInvHap 1.29.0

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]

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scoreInvHap.pdf |scoreInvHap.html✨
scoreInvHap/json (API)

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

Peer review:

Datasets:
  • Refs - Genotype frequency in references
  • SNPsR2 - R2 between the SNPs and the inversion status
  • hetRefs - Heterozygote genotypes in the references
  • info - SNP reference description
  • inversionGR - Inversions' description

On BioConductor:scoreInvHap-1.29.0(bioc 3.21)scoreInvHap-1.28.0(bioc 3.20)

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

snpgeneticsgenomicvariation

4.34 score 11 scripts 204 downloads 2 mentions 13 exports 72 dependencies

Last updated 17 days agofrom:a171cc8e58. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 31 2024
R-4.5-winOKOct 31 2024
R-4.5-linuxOKOct 31 2024
R-4.4-winOKOct 31 2024
R-4.4-macOKOct 31 2024
R-4.3-winOKOct 31 2024
R-4.3-macOKOct 31 2024

Exports:certaintycheckSNPsclassificationclassifSNPsclassifSNPsImputediffscoresmaxscoresnumSNPsplotCallRateplotScorespropSNPsscoreInvHapscores

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecycleMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowsnpStatsSparseArraySummarizedExperimentsurvivalsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc

Inversion genotyping with scoreInvHap

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

Rendered fromscoreInvHap.Rmdusingknitr::rmarkdownon Oct 31 2024.

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