Introduction | Package installation | GDS format introduction | Genomic Data Structure (GDS) | GDSArray, GDSMatrix, and GDSFile | GDSArray, GDSMatrix, and DelayedArray | GDSFile | GDSArray methods | slot accessors. | Available GDS nodes | dim(), dimnames() | [ subsetting | some numeric calculation | Internals: GDSArraySeed | sessionInfo
Package: GDSArray 1.33.0
Xiuwen Zheng
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:
GDSArray_1.33.0.tar.gz
GDSArray_1.33.0.zip(r-4.7)GDSArray_1.33.0.zip(r-4.6)GDSArray_1.33.0.zip(r-4.5)
GDSArray_1.33.0.tgz(r-4.6-any)GDSArray_1.33.0.tgz(r-4.5-any)
GDSArray_1.33.0.tar.gz(r-4.7-any)GDSArray_1.33.0.tar.gz(r-4.6-any)
GDSArray_1.33.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
GDSArray/json (API)
| # Install 'GDSArray' in R: |
| install.packages('GDSArray', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/bioconductor/gdsarray/issues
On BioConductor:GDSArray-1.33.0(bioc 3.24)GDSArray-1.32.0(bioc 3.23)
infrastructuredatarepresentationsequencinggenotypingarray
Last updated from:c911edac10. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 179 | ||
| linux-devel-x86_64 | NOTE | 240 | ||
| source / vignettes | OK | 202 | ||
| linux-release-x86_64 | NOTE | 233 | ||
| macos-release-arm64 | NOTE | 142 | ||
| macos-oldrel-arm64 | NOTE | 114 | ||
| windows-devel | NOTE | 170 | ||
| windows-release | NOTE | 168 | ||
| windows-oldrel | NOTE | 162 | ||
| wasm-release | OK | 114 |
Exports:acquireGDScoerceextract_arrayGDSArraygdsExampleFileNamegdsfileGDSFilegdsfile<-gdsnodesreleaseGDSseedseed<-
Dependencies:abindBiocGenericsBiostringscrayonDelayedArraydigestgdsfmtgenericsGenomicRangesIRangeslatticeMatrixMatrixGenericsmatrixStatsRhpcBLASctlS4ArraysS4VectorsSeqArraySeqinfoSNPRelateSparseArrayXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 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<- gdsfile<-,GDSFile-method 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 |