gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files
Version 1.12.0

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)
Bioconductor views DataImport Infrastructure Software
Date of publicationNone
MaintainerXiuwen Zheng <zhengx@u.washington.edu>
LicenseLGPL-3
Version1.12.0
URL http://corearray.sourceforge.net/ http://github.com/zhengxwen/gdsfmt
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("gdsfmt")

Getting started

Package overview
README.md
R Interface to CoreArray Genomic Data Structure (GDS) Files

Popular man pages

addfolder.gdsn: Add a folder to the GDS node
add.gdsn: Add a new GDS node
closefn.gds: Close a GDS file
delete.gdsn: Delete a GDS node
openfn.gds: Open a GDS file
rename.gdsn: Rename a GDS node
write.gdsn: Write data to a GDS node
See all...

All man pages Function index File listing

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: Get 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

UnitTest Source code
add.gdsn Man page Source code
addfile.gdsn Man page Source code
addfolder.gdsn Man page Source code
append.gdsn Man page Source code
apply.gdsn Man page Source code
assign.gdsn Man page Source code
cache.gdsn Man page Source code
cleanup.gds Man page Source code
closefn.gds Man page Source code
clusterApply.gdsn Man page Source code
cnt.gdsn Man page Source code
compression.gdsn Man page Source code
copyto.gdsn Man page Source code
crayon Source code
createfn.gds Man page Source code
delete.attr.gdsn Man page Source code
delete.gdsn Man page Source code
diagnosis.gds Man page Source code
digest.gdsn Man page Source code
gds.class Man page
gdsfmt Man page
gdsfmt-package Man page
gdsn.class Man page
get Source code
get.attr.gdsn Man page Source code
getfile.gdsn Man page Source code
getfolder.gdsn Man page Source code
index.gdsn Man page Source code
is.element.gdsn Man page Source code
lasterr.gds Man page Source code
ls.gdsn Man page Source code
moveto.gdsn Man page Source code
name.gdsn Man page Source code
objdesp.gdsn Man page Source code
openfn.gds Man page Source code
permdim.gdsn Man page Source code
print.gds.class Man page Source code
print.gdsn.class Man page Source code
put.attr.gdsn Man page Source code
read.gdsn Man page Source code
readex.gdsn Man page Source code
readmode.gdsn Man page Source code
rename.gdsn Man page Source code
setdim.gdsn Man page Source code
show,gdsn.class-method Man page
showfile.gds Man page Source code
summarize.gdsn Man page Source code
sync.gds Man page Source code
system.gds Man page Source code
view_dim Source code
view_dim2 Source code
write.gdsn Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/gdsfmt-main.r
R/methods.r
README.md
build
build/vignette.rds
inst
inst/CITATION
inst/COPYRIGHTS
inst/LGPLv3
inst/doc
inst/doc/gdsfmt_vignette.R
inst/doc/gdsfmt_vignette.Rmd
inst/doc/gdsfmt_vignette.html
inst/include
inst/include/CoreDEF.h
inst/include/R_GDS.h
inst/include/R_GDS2.h
inst/include/R_GDS_CPP.h
inst/include/dTrait.h
inst/include/dType.h
inst/unitTests
inst/unitTests/include.r
inst/unitTests/test_01_datatype.R
inst/unitTests/test_02_dataconvert.R
inst/unitTests/test_03_dimension.R
inst/unitTests/test_04_datareadwrite.R
inst/unitTests/test_05_attribute.R
inst/unitTests/test_06_apply.R
inst/unitTests/test_07_randomaccess.R
inst/unitTests/test_08_miscellaneous.R
inst/unitTests/test_examples.R
inst/unitTests/valid
inst/unitTests/valid/standard.RData
man
man/add.gdsn.Rd
man/addfile.gdsn.Rd
man/addfolder.gdsn.Rd
man/append.gdsn.Rd
man/apply.gdsn.Rd
man/assign.gdsn.Rd
man/cache.gdsn.Rd
man/cleanup.gds.Rd
man/closefn.gds.Rd
man/clusterApply.gdsn.Rd
man/cnt.gdsn.Rd
man/compression.gdsn.Rd
man/copyto.gdsn.Rd
man/createfn.gds.Rd
man/delete.attr.gdsn.Rd
man/delete.gdsn.Rd
man/diagnosis.gds.Rd
man/digest.gdsn.Rd
man/gds.class.Rd
man/gdsfmt-package.Rd
man/gdsn.class.Rd
man/get.attr.gdsn.Rd
man/getfile.gdsn.Rd
man/getfolder.gdsn.Rd
man/index.gdsn.Rd
man/is.element.gdsn.Rd
man/lasterr.gds.Rd
man/ls.gdsn.Rd
man/moveto.gdsn.Rd
man/name.gdsn.Rd
man/objdesp.gdsn.Rd
man/openfn.gds.Rd
man/permdim.gdsn.Rd
man/print.gds.class.Rd
man/put.attr.gdsn.Rd
man/read.gdsn.Rd
man/readex.gdsn.Rd
man/readmode.gdsn.Rd
man/rename.gdsn.Rd
man/setdim.gdsn.Rd
man/showfile.gds.Rd
man/summarize.gdsn.Rd
man/sync.gds.Rd
man/system.gds.Rd
man/write.gdsn.Rd
src
src/CoreArray
src/CoreArray/CoreArray.cpp
src/CoreArray/CoreArray.h
src/CoreArray/dAllocator.cpp
src/CoreArray/dAllocator.h
src/CoreArray/dAny.cpp
src/CoreArray/dAny.h
src/CoreArray/dBase.cpp
src/CoreArray/dBase.h
src/CoreArray/dBit.h
src/CoreArray/dBitGDS.cpp
src/CoreArray/dBitGDS.h
src/CoreArray/dBitGDS_Bit1.h
src/CoreArray/dBitGDS_Bit2.h
src/CoreArray/dBitGDS_Bit24.h
src/CoreArray/dBitGDS_Bit4.h
src/CoreArray/dEndian.cpp
src/CoreArray/dEndian.h
src/CoreArray/dFile.cpp
src/CoreArray/dFile.h
src/CoreArray/dParallel.cpp
src/CoreArray/dParallel.h
src/CoreArray/dParallel_Ext.c
src/CoreArray/dPlatform.cpp
src/CoreArray/dPlatform.h
src/CoreArray/dRealGDS.h
src/CoreArray/dSerial.cpp
src/CoreArray/dSerial.h
src/CoreArray/dStrGDS.h
src/CoreArray/dStream.cpp
src/CoreArray/dStream.h
src/CoreArray/dStruct.cpp
src/CoreArray/dStruct.h
src/CoreArray/dVLIntGDS.cpp
src/CoreArray/dVLIntGDS.h
src/LZ4
src/LZ4/LICENSE
src/LZ4/NEWS
src/LZ4/lz4.c
src/LZ4/lz4.h
src/LZ4/lz4frame.c
src/LZ4/lz4frame.h
src/LZ4/lz4frame_static.h
src/LZ4/lz4hc.c
src/LZ4/lz4hc.h
src/LZ4/lz4opt.h
src/LZ4/xxhash.c
src/LZ4/xxhash.h
src/Makevars
src/Makevars.win
src/R_CoreArray.cpp
src/XZ
src/XZ/api
src/XZ/api/lzma
src/XZ/api/lzma.h
src/XZ/api/lzma/base.h
src/XZ/api/lzma/bcj.h
src/XZ/api/lzma/block.h
src/XZ/api/lzma/check.h
src/XZ/api/lzma/container.h
src/XZ/api/lzma/delta.h
src/XZ/api/lzma/filter.h
src/XZ/api/lzma/hardware.h
src/XZ/api/lzma/index.h
src/XZ/api/lzma/index_hash.h
src/XZ/api/lzma/lzma12.h
src/XZ/api/lzma/stream_flags.h
src/XZ/api/lzma/version.h
src/XZ/api/lzma/vli.h
src/XZ/xz-5.2.3-win.zip
src/XZ/xz-5.2.3.tar.gz
src/ZLIB
src/ZLIB/LICENSE
src/ZLIB/adler32.c
src/ZLIB/compress.c
src/ZLIB/crc32.c
src/ZLIB/crc32.h
src/ZLIB/deflate.c
src/ZLIB/deflate.h
src/ZLIB/infback.c
src/ZLIB/inffast.c
src/ZLIB/inffast.h
src/ZLIB/inffixed.h
src/ZLIB/inflate.c
src/ZLIB/inflate.h
src/ZLIB/inftrees.c
src/ZLIB/inftrees.h
src/ZLIB/trees.c
src/ZLIB/trees.h
src/ZLIB/uncompr.c
src/ZLIB/zconf.h
src/ZLIB/zlib.h
src/ZLIB/zutil.c
src/ZLIB/zutil.h
src/digest.cpp
src/gdsfmt.cpp
tests
tests/runTests.R
vignettes
vignettes/crayon_show.jpg
vignettes/gdsfmt_vignette.Rmd
gdsfmt documentation built on May 20, 2017, 10:42 p.m.

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