Package: VCFArray 1.23.0

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_1.23.0.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-1.23.0(bioc 3.21)VCFArray-1.22.0(bioc 3.20)

infrastructure datarepresentation sequencing variantannotation

4.00 score 1 stars 3 scripts 230 downloads 6 exports 71 dependencies

Last updated 4 months agofrom:2926f6d53d. Checks:1 OK, 7 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 16 2025
R-4.5-win	NOTE	Feb 16 2025
R-4.5-mac	NOTE	Feb 16 2025
R-4.5-linux	NOTE	Feb 16 2025
R-4.4-win	NOTE	Feb 16 2025
R-4.4-mac	NOTE	Feb 16 2025
R-4.3-win	NOTE	Feb 16 2025
R-4.3-mac	NOTE	Feb 16 2025

Exports:coerce extract_array rowRanges show VCFArray vcffile

Dependencies:abind AnnotationDbi askpass BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome cachem cli codetools cpp11 crayon curl DBI DelayedArray fastmap formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 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 Feb 16 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