Package: S4Arrays 1.5.3

Hervé Pagès

S4Arrays: Foundation of array-like containers in Bioconductor

The S4Arrays package defines the Array virtual class to be extended by other S4 classes that wish to implement a container with an array-like semantic. It also provides: (1) low-level functionality meant to help the developer of such container to implement basic operations like display, subsetting, or coercion of their array-like objects to an ordinary matrix or array, and (2) a framework that facilitates block processing of array-like objects (typically on-disk objects).

Authors:Hervé Pagès [aut, cre], Jacques Serizay [ctb]

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S4Arrays.pdf |S4Arrays.html✨
S4Arrays/json (API)
NEWS

# Install 'S4Arrays' in R:

install.packages('S4Arrays', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bioconductor/s4arrays/issues

On BioConductor:S4Arrays-1.5.2(bioc 3.20)S4Arrays-1.4.1(bioc 3.19)

bioconductor-package

63 exports 12.58 score 7 dependencies 1171 dependents

Last updated 8 days agofrom:b306a0bdab

Exports:abind acbind aperm aperm.ArbitraryArrayGrid aperm.DummyArrayGrid aperm.RegularArrayGrid aperm2 arbind ArbitraryArrayGrid ArrayViewport as.array.Array as.character.Array as.character.ArrayGrid as.complex.Array as.data.frame as.data.frame.Array as.integer.Array as.logical.Array as.matrix as.matrix.Array as.numeric.Array as.raw.Array as.vector.Array bindROWS cbind coerce colsum dims downsample drop DummyArrayGrid DummyArrayViewport end extract_array is_sparse is_sparse<-isEmpty Lindex2Mindex makeNindexFromArrayViewport mapToGrid mapToRef maxlength mean Mindex2Lindex nchar ranges rbind read_block read_block_as_dense refdim RegularArrayGrid rowsum show showAsCell start t t.Array tune_Array_dims type var which width write_block

Dependencies:abind BiocGenerics crayon IRanges lattice Matrix S4Vectors

A quick overview of the S4Arrays package

Hervé Pagès

Rendered fromS4Arrays_quick_overview.Rmdusingknitr::rmarkdownon Jul 04 2024.

Last update: 2024-04-08
Started: 2023-03-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generalized permutation of the dimensions of an array	aperm2
Manipulation of array selections	array selection array selections array_selection array_selections L-index Lindex Lindex2Mindex M-index Mindex Mindex2Lindex N-index Nindex
ArrayGrid and ArrayViewport objects	aperm,ArbitraryArrayGrid-method aperm,DummyArrayGrid-method aperm,RegularArrayGrid-method aperm.ArbitraryArrayGrid aperm.DummyArrayGrid aperm.RegularArrayGrid ArbitraryArrayGrid ArbitraryArrayGrid-class ArrayGrid ArrayGrid-class ArrayViewport ArrayViewport-class as.character,ArrayGrid-method as.character.ArrayGrid class:ArbitraryArrayGrid class:ArrayGrid class:ArrayViewport class:DummyArrayGrid class:DummyArrayViewport class:RegularArrayGrid class:SafeArrayViewport classNameForDisplay,ArrayViewport-method dim,ArbitraryArrayGrid-method dim,ArrayViewport-method dim,DummyArrayGrid-method dim,RegularArrayGrid-method dims dims,ArrayGrid-method downsample downsample,ArbitraryArrayGrid-method downsample,RegularArrayGrid-method DummyArrayGrid DummyArrayGrid-class DummyArrayViewport DummyArrayViewport-class end,ArrayViewport-method lengths,ArrayGrid-method lengths,DummyArrayGrid-method makeNindexFromArrayViewport maxlength maxlength,ANY-method maxlength,ArbitraryArrayGrid-method maxlength,RegularArrayGrid-method ranges,DummyArrayViewport-method ranges,SafeArrayViewport-method refdim refdim,ArbitraryArrayGrid-method refdim,ArrayViewport-method refdim,DummyArrayGrid-method refdim,RegularArrayGrid-method RegularArrayGrid RegularArrayGrid-class SafeArrayViewport SafeArrayViewport-class show,ArrayGrid-method show,ArrayViewport-method start,ArrayViewport-method width,ArrayViewport-method
Combine multidimensional array-like objects	abind abind,ANY-method acbind acbind,ANY-method arbind arbind,ANY-method bind arrays bind-arrays
Check for sparse representation	is_sparse is_sparse,ANY-method is_sparse,dgCMatrix-method is_sparse,dgRMatrix-method is_sparse,lgCMatrix-method is_sparse,lgRMatrix-method is_sparse<-
Read array blocks	read_block read_block_as_dense read_block_as_dense,ANY-method
Compute column/row sums of a matrix-like object, for groups of rows/columns	colsum colsum,ANY-method rowsum
Get the type of the elements of an array-like object	type type,ANY-method type,DataFrame-method
Write array blocks	write_block write_block,ANY-method