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

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This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms and include 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 with less than 8 bits, since a single genetic/genomic variant, like single-nucleotide polymorphism, usually occupies fewer bits than a byte. Data compression and decompression are also supported with relatively efficient random access. It is allowed to read a GDS file in parallel with multiple R processes supported by the parallel package.

Author
Xiuwen Zheng [aut, cre], Jean-loup Gailly [ctb] (zlib library), Mark Adler [ctb] (zlib library), Yann Collet [ctb] (LZ4 library)
Date of publication
2014-12-25 11:33:28
Maintainer
Xiuwen Zheng <zhengx@u.washington.edu>
License
LGPL-3
Version
1.1.3
URLs

View on R-Forge

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
createfn.gds
Create a GDS file
delete.attr.gdsn
Delete an attribute
delete.gdsn
Delete a GDS node
diagnosis.gds
Diagnose the GDS file
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
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
Diagnose the GDS file
name.gdsn
Return the variable name of a node
objdesp.gdsn
Variable description
openfn.gds
Open a GDS file
print.gds.class
Show the information of class "gds.class"
print.gdsn.class
Show the information of class "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
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/README.md
gdsfmt/inst
gdsfmt/inst/CITATION
gdsfmt/inst/COPYRIGHTS
gdsfmt/inst/LGPLv3
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/runit.01.datatype.r
gdsfmt/inst/unitTests/runit.02.dataconvert.r
gdsfmt/inst/unitTests/runit.03.dimension.r
gdsfmt/inst/unitTests/runit.04.datareadwrite.r
gdsfmt/inst/unitTests/runit.05.attribute.r
gdsfmt/inst/unitTests/runit.06.apply.r
gdsfmt/inst/unitTests/runit.07.randomzip.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/createfn.gds.Rd
gdsfmt/man/delete.attr.gdsn.Rd
gdsfmt/man/delete.gdsn.Rd
gdsfmt/man/diagnosis.gds.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/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/print.gds.class.Rd
gdsfmt/man/print.gdsn.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/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/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/CoreGDS.cpp
gdsfmt/src/CoreGDS.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/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/gdsfmt.cpp
gdsfmt/src/gdsfmt_deprecated.h
gdsfmt/tests
gdsfmt/tests/runTests.R