Package: VCFArray 1.27.0

Qian Liu

VCFArray: Representing on-disk / remote VCF files as array-like objects

VCFArray extends the DelayedArray to represent VCF data entries as array-like objects with on-disk / remote VCF file as backend. Data entries from VCF files, including info fields, FORMAT fields, and the fixed columns (REF, ALT, QUAL, FILTER) could be converted into VCFArray instances with different dimensions.

Authors:Qian Liu [aut, cre], Martin Morgan [aut]

VCFArray_1.27.0.tar.gz
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VCFArray.pdf |VCFArray.html✨
VCFArray/json (API)
NEWS

# Install 'VCFArray' in R:

install.packages('VCFArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/liubuntu/vcfarray/issues

On BioConductor:VCFArray-1.27.0(bioc 3.23)VCFArray-1.26.0(bioc 3.22)

infrastructure datarepresentation sequencing variantannotation

4.00 score 1 stars 3 scripts 295 downloads 6 exports 73 dependencies

Last updated from:c9fb606916. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Total time
bioc-checks	ERROR	189
linux-devel-x86_64	NOTE	388
source / vignettes	OK	312
linux-release-x86_64	NOTE	497
macos-release-arm64	NOTE	244
macos-oldrel-arm64	NOTE	276
windows-devel	NOTE	343
windows-release	NOTE	316
windows-oldrel	NOTE	317
wasm-release	OK	167

Exports:coerce extract_array rowRanges show VCFArray vcffile

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 GenomeInfoDb GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges glue httr IRanges jsonlite KEGGREST lambda.r lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys UCSC.utils VariantAnnotation vctrs XML XVector yaml

VCFArray: DelayedArray objects with on-disk/remote VCF backend

Qian Liu, Martin Morgan

Rendered fromVCFArray.Rmdusingknitr::rmarkdownon Nov 23 2025.

Last update: 2021-10-05
Started: 2018-08-22

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
VCFArraySeed or VCFArray related methods, slot getters and setters.	dim,VCFArraySeed-method dimnames,VCFArraySeed-method rowRanges,VCFArray-method rowRanges,VCFArraySeed-method show,VCFArraySeed-method vcffile vcffile,VCFArray vcffile,VCFArray-method vcffile,VCFArraySeed vcffile,VCFArraySeed-method
VCFArray constructor and coercion methods.	coerce coerce,ANY,VCFMatrix-method coerce,VCFArray,VCFMatrix-method coerce,VCFMatrix,VCFArray-method extract_array extract_array,VCFArraySeed-method matrixClass,VCFArray-method VCFArray VCFArray-class VCFArray-method VCFMatrix VCFMatrix-class