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

Functions

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

Files

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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