Package: VCFArray 1.29.0

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_1.29.0.tar.gz
VCFArray_1.29.0.zip(r-4.7)VCFArray_1.29.0.zip(r-4.6)VCFArray_1.29.0.zip(r-4.5)
VCFArray_1.29.0.tgz(r-4.6-any)VCFArray_1.29.0.tgz(r-4.5-any)
VCFArray_1.29.0.tar.gz(r-4.7-any)VCFArray_1.29.0.tar.gz(r-4.6-any)
VCFArray_1.29.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
VCFArray/json (API)

# 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-1.29.0(bioc 3.24)VCFArray-1.28.0(bioc 3.23)

infrastructure datarepresentation sequencing variantannotation

4.00 score 1 stars 3 scripts 6 exports 72 dependencies

Last updated from:e9c7ac343f. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	215
linux-devel-x86_64	NOTE	425
source / vignettes	OK	307
linux-release-x86_64	NOTE	448
macos-release-arm64	NOTE	288
macos-oldrel-arm64	NOTE	247
windows-devel	NOTE	299
windows-release	NOTE	294
windows-oldrel	NOTE	317
wasm-release	OK	154

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 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

Rendered fromVCFArray.Rmdusingknitr::rmarkdown

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