Package: gdsfmt 1.43.0

Xiuwen Zheng

gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.

Authors:Xiuwen Zheng [aut, cre], Stephanie Gogarten [ctb], Jean-loup Gailly and Mark Adler [ctb], Yann Collet [ctb], xz contributors [ctb]

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

# Install 'gdsfmt' in R:

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

Bug tracker:https://github.com/zhengxwen/gdsfmt/issues

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:gdsfmt-1.43.0(bioc 3.21)gdsfmt-1.42.0(bioc 3.20)

infrastructure dataimport bioinformatics gds-format genomics cpp

11.25 score 18 stars 30 packages 922 scripts 3.4k downloads 23 mentions 47 exports 0 dependencies

Last updated 2 months agofrom:84cf1468ac. Checks:OK: 7 WARNING: 2. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win-x86_64	OK	Nov 29 2024
R-4.5-linux-x86_64	OK	Nov 29 2024
R-4.4-win-x86_64	OK	Nov 29 2024
R-4.4-mac-x86_64	WARNING	Nov 29 2024
R-4.4-mac-aarch64	OK	Nov 29 2024
R-4.3-win-x86_64	OK	Nov 29 2024
R-4.3-mac-x86_64	WARNING	Nov 29 2024
R-4.3-mac-aarch64	OK	Nov 29 2024

Exports:add.gdsn addfile.gdsn addfolder.gdsn append.gdsn apply.gdsn assign.gdsn cache.gdsn cleanup.gds closefn.gds clusterApply.gdsn cnt.gdsn compression.gdsn copyto.gdsn createfn.gds delete.attr.gdsn delete.gdsn diagnosis.gds digest.gdsn exist.gdsn get.attr.gdsn getfile.gdsn getfolder.gdsn index.gdsn is.element.gdsn is.sparse.gdsn lasterr.gds ls.gdsn moveto.gdsn name.gdsn objdesp.gdsn openfn.gds permdim.gdsn print.gds.class print.gdsn.class put.attr.gdsn read.gdsn readex.gdsn readmode.gdsn rename.gdsn setdim.gdsn show showfile.gds summarize.gdsn sync.gds system.gds unload.gdsn write.gdsn

Dependencies:

R Interface to CoreArray Genomic Data Structure (GDS) Files

Dr. Xiuwen Zheng

Rendered fromgdsfmt.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2022-07-15
Started: 2019-10-14

Help page	Topics
R Interface to CoreArray Genomic Data Structure (GDS) files	gdsfmt-package gdsfmt
Add a new GDS node	add.gdsn
Add a GDS node with a file	addfile.gdsn
Add a folder to the GDS node	addfolder.gdsn
Append data to a specified variable	append.gdsn
Apply functions over margins	apply.gdsn
Assign/append data to a GDS node	assign.gdsn
Caching variable data	cache.gdsn
Clean up fragments	cleanup.gds
Close a GDS file	closefn.gds
Apply functions over matrix margins in parallel	clusterApply.gdsn
Return the number of child nodes	cnt.gdsn
Modify compression mode	compression.gdsn
Copy GDS nodes	copyto.gdsn
Create a GDS file	createfn.gds
Delete attribute(s)	delete.attr.gdsn
Delete a GDS node	delete.gdsn
Diagnose the GDS file	diagnosis.gds
create hash function digests	digest.gdsn
Return whether the path exists or not	exist.gdsn
the class of GDS file	gds.class
the class of variable node in the GDS file	gdsn.class
Get attributes	get.attr.gdsn
Output a file from a stream container	getfile.gdsn
Get the folder	getfolder.gdsn
Get the specified node	index.gdsn
whether the elements are in a set	is.element.gdsn
whether a sparse array or not	is.sparse.gdsn
Return the last error message	lasterr.gds
Return the names of child nodes	ls.gdsn
Relocate a GDS node	moveto.gdsn
Return the variable name of a node	name.gdsn
Variable description	objdesp.gdsn
Open a GDS file	openfn.gds
Array Transposition	permdim.gdsn
Show the information of class "gds.class" and "gdsn.class"	print.gds.class print.gdsn.class show,gdsn.class-method
Add an attribute into a GDS node	put.attr.gdsn
Read data field of a GDS node	read.gdsn
Read data field of a GDS node with a selection	readex.gdsn
Switch to read mode in the compression settings	readmode.gdsn
Rename a GDS node	rename.gdsn
Set the dimension of data field	setdim.gdsn
Enumerate opened GDS files	showfile.gds
GDS object Summaries	summarize.gdsn
Synchronize a GDS file	sync.gds
Get the parameters in the GDS system	system.gds
Unload a GDS node	unload.gdsn
Write data to a GDS node	write.gdsn

Package: gdsfmt 1.43.0

gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

R Interface to CoreArray Genomic Data Structure (GDS) Files

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