Package: GDSArray 1.27.0

Qian Liu

GDSArray: Representing GDS files as array-like objects

GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.

Authors:Qian Liu [aut, cre], Martin Morgan [aut], Hervé Pagès [aut], Xiuwen Zheng [aut]

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GDSArray.pdf |GDSArray.html✨
GDSArray/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/bioconductor/gdsarray/issues

On BioConductor:GDSArray-1.27.0(bioc 3.21)GDSArray-1.26.0(bioc 3.20)

infrastructuredatarepresentationsequencinggenotypingarray

6.65 score 5 stars 2 packages 8 scripts 498 downloads 12 exports 30 dependencies

Last updated 2 months agofrom:ec35b07929. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 22 2024
R-4.5-winWARNINGNov 22 2024
R-4.5-linuxWARNINGDec 22 2024
R-4.4-winWARNINGNov 22 2024
R-4.4-macWARNINGDec 22 2024
R-4.3-winWARNINGNov 22 2024
R-4.3-macWARNINGDec 22 2024

Exports:acquireGDScoerceextract_arrayGDSArraygdsExampleFileNamegdsfileGDSFilegdsfile<-gdsnodesreleaseGDSseedseed<-

Dependencies:abindaskpassBiocGenericsBiostringscrayoncurlDelayedArraygdsfmtgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangeshttrIRangesjsonlitelatticeMatrixMatrixGenericsmatrixStatsmimeopensslR6S4ArraysS4VectorsSeqArraySNPRelateSparseArraysysUCSC.utilsXVector

GDSArray: Representing GDS files as array-like objects

Qian Liu, Hervé Pagès, Martin Morgan

Rendered fromGDSArray.Rmdusingknitr::rmarkdownon Dec 22 2024.

Last update: 2024-05-22
Started: 2018-03-01

Readme and manuals

Help Manual

Help pageTopics
Acquire the GDS file connection in R in the 'gds.class' class.acquireGDS releaseGDS
GDSArray constructor and coercion methods.coerce coerce,ANY,GDSMatrix-method coerce,GDSArray,GDSMatrix-method coerce,GDSMatrix,GDSArray-method extract_array extract_array,GDSArraySeed-method GDSArray GDSArray-class GDSArray-data GDSArray-method gdsExampleFileName GDSMatrix GDSMatrix-class matrixClass,GDSArray-method
GDSFile constructor and methods.$,GDSFile-method GDSFile GDSFile,gdsfile-method gdsfile,GDSFile-method GDSFile-class GDSFile-constructor GDSFile-method gdsfile<- gdsnodes gdsnodes,ANY-method gdsnodes,GDSFile-method
GDSArraySeed or GDSArray related methods, slot getters and setters.gdsfile gdsfile,DelayedArray-method gdsfile,GDSArray-method gdsfile,GDSArraySeed-method seed,GDSArray-method seed<-,GDSArray-method