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

This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are 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.

AuthorXiuwen Zheng [aut, cre], Stephanie Gogarten [ctb], Jean-loup Gailly and Mark Adler [ctb] (for the included zlib sources), Yann Collet [ctb] (for the included LZ4 sources), xz contributors (for the included liblzma sources)
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseLGPL-3
Version1.10.1
http://corearray.sourceforge.net/, http://github.com/zhengxwen/gdsfmt

View on Bioconductor

Man pages

addfile.gdsn: Add a GDS node with a file

addfolder.gdsn: Add a folder to the GDS node

add.gdsn: Add a new GDS node

append.gdsn: Append data to a specified variable

apply.gdsn: Apply functions over margins

assign.gdsn: Assign/append data to a GDS node

cache.gdsn: Caching variable data

cleanup.gds: Clean up fragments

closefn.gds: Close a GDS file

clusterApply.gdsn: Apply functions over matrix margins in parallel

cnt.gdsn: Return the number of child nodes

compression.gdsn: Modify compression mode

copyto.gdsn: Copy GDS nodes

createfn.gds: Create a GDS file

delete.attr.gdsn: Delete attribute(s)

delete.gdsn: Delete a GDS node

diagnosis.gds: Diagnose the GDS file

digest.gdsn: create hash function digests

gds.class: the class of GDS file

gdsfmt-package: R Interface to CoreArray Genomic Data Structure (GDS) files

gdsn.class: the class of variable node in the GDS file

get.attr.gdsn: Get attributes

getfile.gdsn: Output a file from a stream container

getfolder.gdsn: Get the folder

index.gdsn: Return the specified node

is.element.gdsn: whether the elements are in a set

lasterr.gds: Return the last error message

ls.gdsn: Return the names of child nodes

moveto.gdsn: Relocate a GDS node

name.gdsn: Return the variable name of a node

objdesp.gdsn: Variable description

openfn.gds: Open a GDS file

permdim.gdsn: Array Transposition

print.gds.class: Show the information of class "gds.class" and "gdsn.class"

put.attr.gdsn: Add an attribute into a GDS node

readex.gdsn: Read data field of a GDS node with a selection

read.gdsn: Read data field of a GDS node

readmode.gdsn: Switch to read mode in the compression settings

rename.gdsn: Rename a GDS node

setdim.gdsn: Set the dimension of data field

showfile.gds: Enumerate opened GDS files

summarize.gdsn: GDS object Summaries

sync.gds: Synchronize a GDS file

system.gds: Get the parameters in the GDS system

write.gdsn: Write data to a GDS node

Files in this package

gdsfmt/DESCRIPTION
gdsfmt/NAMESPACE
gdsfmt/NEWS
gdsfmt/R
gdsfmt/R/gdsfmt-main.r
gdsfmt/R/methods.r
gdsfmt/README.md
gdsfmt/build
gdsfmt/build/vignette.rds
gdsfmt/inst
gdsfmt/inst/CITATION
gdsfmt/inst/COPYRIGHTS
gdsfmt/inst/LGPLv3
gdsfmt/inst/doc
gdsfmt/inst/doc/gdsfmt_vignette.R
gdsfmt/inst/doc/gdsfmt_vignette.Rmd
gdsfmt/inst/doc/gdsfmt_vignette.html
gdsfmt/inst/include
gdsfmt/inst/include/CoreDEF.h
gdsfmt/inst/include/R_GDS.h
gdsfmt/inst/include/R_GDS2.h
gdsfmt/inst/include/R_GDS_CPP.h
gdsfmt/inst/include/dTrait.h
gdsfmt/inst/include/dType.h
gdsfmt/inst/unitTests
gdsfmt/inst/unitTests/include.r
gdsfmt/inst/unitTests/test_01_datatype.R
gdsfmt/inst/unitTests/test_02_dataconvert.R
gdsfmt/inst/unitTests/test_03_dimension.R
gdsfmt/inst/unitTests/test_04_datareadwrite.R
gdsfmt/inst/unitTests/test_05_attribute.R
gdsfmt/inst/unitTests/test_06_apply.R
gdsfmt/inst/unitTests/test_07_randomaccess.R
gdsfmt/inst/unitTests/test_08_miscellaneous.R
gdsfmt/inst/unitTests/test_examples.R
gdsfmt/inst/unitTests/valid
gdsfmt/inst/unitTests/valid/standard.RData
gdsfmt/man
gdsfmt/man/add.gdsn.Rd gdsfmt/man/addfile.gdsn.Rd gdsfmt/man/addfolder.gdsn.Rd gdsfmt/man/append.gdsn.Rd gdsfmt/man/apply.gdsn.Rd gdsfmt/man/assign.gdsn.Rd gdsfmt/man/cache.gdsn.Rd gdsfmt/man/cleanup.gds.Rd gdsfmt/man/closefn.gds.Rd gdsfmt/man/clusterApply.gdsn.Rd gdsfmt/man/cnt.gdsn.Rd gdsfmt/man/compression.gdsn.Rd gdsfmt/man/copyto.gdsn.Rd gdsfmt/man/createfn.gds.Rd gdsfmt/man/delete.attr.gdsn.Rd gdsfmt/man/delete.gdsn.Rd gdsfmt/man/diagnosis.gds.Rd gdsfmt/man/digest.gdsn.Rd gdsfmt/man/gds.class.Rd gdsfmt/man/gdsfmt-package.Rd gdsfmt/man/gdsn.class.Rd gdsfmt/man/get.attr.gdsn.Rd gdsfmt/man/getfile.gdsn.Rd gdsfmt/man/getfolder.gdsn.Rd gdsfmt/man/index.gdsn.Rd gdsfmt/man/is.element.gdsn.Rd gdsfmt/man/lasterr.gds.Rd gdsfmt/man/ls.gdsn.Rd gdsfmt/man/moveto.gdsn.Rd gdsfmt/man/name.gdsn.Rd gdsfmt/man/objdesp.gdsn.Rd gdsfmt/man/openfn.gds.Rd gdsfmt/man/permdim.gdsn.Rd gdsfmt/man/print.gds.class.Rd gdsfmt/man/put.attr.gdsn.Rd gdsfmt/man/read.gdsn.Rd gdsfmt/man/readex.gdsn.Rd gdsfmt/man/readmode.gdsn.Rd gdsfmt/man/rename.gdsn.Rd gdsfmt/man/setdim.gdsn.Rd gdsfmt/man/showfile.gds.Rd gdsfmt/man/summarize.gdsn.Rd gdsfmt/man/sync.gds.Rd gdsfmt/man/system.gds.Rd gdsfmt/man/write.gdsn.Rd
gdsfmt/src
gdsfmt/src/CoreArray
gdsfmt/src/CoreArray/CoreArray.cpp
gdsfmt/src/CoreArray/CoreArray.h
gdsfmt/src/CoreArray/dAllocator.cpp
gdsfmt/src/CoreArray/dAllocator.h
gdsfmt/src/CoreArray/dAny.cpp
gdsfmt/src/CoreArray/dAny.h
gdsfmt/src/CoreArray/dBase.cpp
gdsfmt/src/CoreArray/dBase.h
gdsfmt/src/CoreArray/dBit.h
gdsfmt/src/CoreArray/dBitGDS.cpp
gdsfmt/src/CoreArray/dBitGDS.h
gdsfmt/src/CoreArray/dBitGDS_Bit1.h
gdsfmt/src/CoreArray/dBitGDS_Bit2.h
gdsfmt/src/CoreArray/dBitGDS_Bit24.h
gdsfmt/src/CoreArray/dBitGDS_Bit4.h
gdsfmt/src/CoreArray/dEndian.cpp
gdsfmt/src/CoreArray/dEndian.h
gdsfmt/src/CoreArray/dFile.cpp
gdsfmt/src/CoreArray/dFile.h
gdsfmt/src/CoreArray/dParallel.cpp
gdsfmt/src/CoreArray/dParallel.h
gdsfmt/src/CoreArray/dParallel_Ext.c
gdsfmt/src/CoreArray/dPlatform.cpp
gdsfmt/src/CoreArray/dPlatform.h
gdsfmt/src/CoreArray/dRealGDS.h
gdsfmt/src/CoreArray/dSerial.cpp
gdsfmt/src/CoreArray/dSerial.h
gdsfmt/src/CoreArray/dStrGDS.h
gdsfmt/src/CoreArray/dStream.cpp
gdsfmt/src/CoreArray/dStream.h
gdsfmt/src/CoreArray/dStruct.cpp
gdsfmt/src/CoreArray/dStruct.h
gdsfmt/src/CoreArray/dVLIntGDS.cpp
gdsfmt/src/CoreArray/dVLIntGDS.h
gdsfmt/src/LZ4
gdsfmt/src/LZ4/LICENSE
gdsfmt/src/LZ4/NEWS
gdsfmt/src/LZ4/lz4.c
gdsfmt/src/LZ4/lz4.h
gdsfmt/src/LZ4/lz4frame.c
gdsfmt/src/LZ4/lz4frame.h
gdsfmt/src/LZ4/lz4frame_static.h
gdsfmt/src/LZ4/lz4hc.c
gdsfmt/src/LZ4/lz4hc.h
gdsfmt/src/LZ4/xxhash.c
gdsfmt/src/LZ4/xxhash.h
gdsfmt/src/Makevars
gdsfmt/src/Makevars.win
gdsfmt/src/R_CoreArray.cpp
gdsfmt/src/XZ
gdsfmt/src/XZ/api
gdsfmt/src/XZ/api/lzma
gdsfmt/src/XZ/api/lzma.h
gdsfmt/src/XZ/api/lzma/base.h
gdsfmt/src/XZ/api/lzma/bcj.h
gdsfmt/src/XZ/api/lzma/block.h
gdsfmt/src/XZ/api/lzma/check.h
gdsfmt/src/XZ/api/lzma/container.h
gdsfmt/src/XZ/api/lzma/delta.h
gdsfmt/src/XZ/api/lzma/filter.h
gdsfmt/src/XZ/api/lzma/hardware.h
gdsfmt/src/XZ/api/lzma/index.h
gdsfmt/src/XZ/api/lzma/index_hash.h
gdsfmt/src/XZ/api/lzma/lzma12.h
gdsfmt/src/XZ/api/lzma/stream_flags.h
gdsfmt/src/XZ/api/lzma/version.h
gdsfmt/src/XZ/api/lzma/vli.h
gdsfmt/src/XZ/xz-5.2.1-win.zip
gdsfmt/src/XZ/xz-5.2.2.tar.gz
gdsfmt/src/ZLIB
gdsfmt/src/ZLIB/LICENSE
gdsfmt/src/ZLIB/adler32.c
gdsfmt/src/ZLIB/compress.c
gdsfmt/src/ZLIB/crc32.c
gdsfmt/src/ZLIB/crc32.h
gdsfmt/src/ZLIB/deflate.c
gdsfmt/src/ZLIB/deflate.h
gdsfmt/src/ZLIB/infback.c
gdsfmt/src/ZLIB/inffast.c
gdsfmt/src/ZLIB/inffast.h
gdsfmt/src/ZLIB/inffixed.h
gdsfmt/src/ZLIB/inflate.c
gdsfmt/src/ZLIB/inflate.h
gdsfmt/src/ZLIB/inftrees.c
gdsfmt/src/ZLIB/inftrees.h
gdsfmt/src/ZLIB/trees.c
gdsfmt/src/ZLIB/trees.h
gdsfmt/src/ZLIB/uncompr.c
gdsfmt/src/ZLIB/zconf.h
gdsfmt/src/ZLIB/zlib.h
gdsfmt/src/ZLIB/zutil.c
gdsfmt/src/ZLIB/zutil.h
gdsfmt/src/digest.cpp
gdsfmt/src/gdsfmt.cpp
gdsfmt/tests
gdsfmt/tests/runTests.R
gdsfmt/vignettes
gdsfmt/vignettes/crayon_show.jpg
gdsfmt/vignettes/gdsfmt_vignette.Rmd

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