Package: scoreInvHap 1.35.0

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_1.35.0.tar.gz
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scoreInvHap_1.35.0.tgz(r-4.6-any)scoreInvHap_1.35.0.tgz(r-4.5-any)
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scoreInvHap_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scoreInvHap/json (API)

# Install 'scoreInvHap' in R:

install.packages('scoreInvHap', repos = c('https://bioc.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.

snp genetics genomicvariation

4.38 score 12 scripts 417 downloads 2 mentions 13 exports 71 dependencies

Last updated from:c1c7fd2423. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	211
linux-devel-x86_64	OK	383
source / vignettes	OK	275
linux-release-x86_64	OK	435
macos-release-arm64	OK	273
macos-oldrel-arm64	OK	184
windows-devel	OK	280
windows-release	OK	301
windows-oldrel	OK	339
wasm-release	OK	150

Exports:certainty checkSNPs classification classifSNPs classifSNPsImpute diffscores maxscores numSNPs plotCallRate plotScores propSNPs scoreInvHap scores

Dependencies:abind AnnotationDbi askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cigarillo cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomicAlignments GenomicFeatures GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow snpStats SparseArray SummarizedExperiment survival sys VariantAnnotation vctrs XML XVector yaml

Inversion genotyping with scoreInvHap

Rendered fromscoreInvHap.Rmdusingknitr::rmarkdown

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

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Adapt references to imputed data	adaptRefs
Check genotype object	checkSNPs
Get similarity scores and probability	classifSNPs classifSNPsImpute
Compute all similarity scores for a sample	computeScore
Solve genotypes discrepancies	correctAlleleTable
Compute the allele table	getAlleleTable
Get genotypes table	getGenotypesTable
Get the inversion status of a sample	getInvStatus
Heterozygote genotypes in the references	hetRefs
SNP reference description	info
Inversions' description	inversionGR
Modify feature data from VCF	prepareMap
Genotype frequency in references	Refs
scoreInvHap: package to get inversion status of predefined regions.	scoreInvHap
scoreInvHapRes instances	certainty 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 status	SNPsR2