package ‘gdsfmt’package ‘gdsfmt’ february 19, 2013 type package title corearray genomic data...
TRANSCRIPT
Package ‘gdsfmt’February 19, 2013
Type Package
Title CoreArray Genomic Data Structure (GDS) R Interface
Version 0.9.12
Date 2013-02-15
Depends R (>= 2.12.0)
Suggests parallel, snow, RUnit
Author Xiuwen Zheng
Maintainer Xiuwen Zheng <[email protected]>
Description CoreArray project is to develop portable and scalablestorage technologies for bioinformatics data, allowing parallelcomputing at the multicore and cluster levels.
License LGPL-3
URL http://corearray.sourceforge.net/
Forums http://sourceforge.net/projects/corearray/forums
NeedsCompilation yes
Repository CRAN
Date/Publication 2013-02-19 15:25:25
R topics documented:gdsfmt-package . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2add.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4addfile.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6append.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8apply.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 9assign.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11
1
2 gdsfmt-package
cleanup.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12closefn.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13clusterApply.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 14cnt.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16compression.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17createfn.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18delete.attr.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19delete.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20gds.class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21gdsn.class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21gdsUnitTest . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22get.attr.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22getfile.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23index.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 24lasterr.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 25ls.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26name.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 27objdesp.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28openfn.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29print.gds.class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30print.gdsn.class . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 31put.attr.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32read.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33readex.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 34readmode.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35rename.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36setdim.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37sync.gds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38write.gdsn . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 39
Index 41
gdsfmt-package CoreArray Genomic Data Structure (GDS) R Interface
Description
R interface of CoreArray GDS is based on the CoreArray project initiated and developed from 2007.
Details
Package: gdsfmtType: PackageVersion: 0.9.12Date: 2013-02-18License: LGPL version 3
gdsfmt-package 3
R interface of CoreArray GDS is based on the CoreArray project initiated and developed by XiuwenZheng from 2007. The CoreArray project is to develop portable, scalable, bioinformatics datavisualization and storage technologies.
R is the most popular statistical environment, but one not necessarily optimized for high perfor-mance or parallel computing which ease the burden of large-scale calculations. To support efficientdata management in parallel for numerical genomic data, we developed the Genomic Data Structure(GDS) file format. gdsfmt provides fundamental functions to support accessing data in parallel, andallows future R packages to call these functions.
Forums: http://sourceforge.net/projects/corearray/forums
Author(s)
Xiuwen Zheng <[email protected]>
References
http://corearray.sourceforge.net
Xiuwen Zheng, David Levine, Jess Shen, Stephanie M. Gogarten, Cathy Laurie, Bruce S. Weir. AHigh-performance Computing Toolset for Relatedness and Principal Component Analysis of SNPData. Bioinformatics 2012; doi: 10.1093/bioinformatics/bts606
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))L <- -2500:2499
# commom typesadd.gdsn(f, "int", val=as.integer(1:10000), compress="ZIP", closezip=TRUE)add.gdsn(f, "int.matrix", val=matrix(L, nrow=100, ncol=50))add.gdsn(f, "mat", val=matrix(1:(10*6), nrow=10))add.gdsn(f, "double", val=seq(1, 1000, 0.4))add.gdsn(f, "character", val=c("int", "double", "logical", "factor"))add.gdsn(f, "logical", val=rep(c(TRUE, FALSE, NA), 50))add.gdsn(f, "factor", val=as.factor(c(letters, NA, "AA", "CC")))add.gdsn(f, "NA", val=rep(NA, 10))add.gdsn(f, "NaN", val=c(rep(NaN, 20), 1:20))add.gdsn(f, "bit2-matrix", val=matrix(L[1:5000], nrow=50, ncol=100), storage="bit2")# list and data.frameadd.gdsn(f, "list", val=list(X=1:10, Y=seq(1, 10, 0.25)))add.gdsn(f, "data.frame", val=data.frame(X=1:19, Y=seq(1, 10, 0.5)))
# save a .RData objectobj <- list(X=1:10, Y=seq(1, 10, 0.1))save(obj, file="tmp.RData")addfile.gdsn(f, "tmp.RData", filename="tmp.RData")
f
read.gdsn(index.gdsn(f, "list"))
4 add.gdsn
read.gdsn(index.gdsn(f, "list/Y"))read.gdsn(index.gdsn(f, "data.frame"))read.gdsn(index.gdsn(f, "mat"))
# Apply functions over columns of matrixtmp <- apply.gdsn(index.gdsn(f, "mat"), margin=2, FUN=function(x) print(x))tmp <- apply.gdsn(index.gdsn(f, "mat"), margin=2,selection = list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)),FUN=function(x) print(x))
closefn.gds(f)
add.gdsn Add a GDS node
Description
Adds a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
add.gdsn(node, name, val = NULL, storage = storage.mode(val), valdim = NULL,compress = c("", "ZIP", "ZIP.fast", "ZIP.default", "ZIP.max"), closezip = FALSE)
Arguments
node an object of class gdsn.class or gds.class: "gdsn" – the node of hierarchicalstructure; "gdsclass" – the root of hieracrchical structure
name the variable name of the added node
val the R value can be vector, list, data.frame
storage to specify data type (not case-sensitive): integer ( signed integer: "int8", "int16","int24", "int32", "int64", "sbit2", "sbit3", "sbit4", "sbit5", "sbit6", "sbit7", "sbit8","sbit9", "sbit10", "sbit11", "sbit12", "sbit13", "sbit14", "sbit15", "sbit16", "sbit24","sbit32", "sbit64" ; unsigned integer: "uint8", "uint16", "uint24", "uint32", "uint64","bit1", "bit2", "bit3", "bit4", "bit5", "bit6", "bit7", "bit8", "bit9", "bit10", "bit11","bit12", "bit13", "bit14", "bit15", "bit16", "bit24", "bit32", "bit64" ); float ("float32","float64"), string (variable-length: "string", "string16", "string32"; fixed-length:"fstring", "fstring16", "fstring32"). Or "integer" (="int32"), "float" (="float32"),"double" (="float64"), "character" (="string"), "logical", "list", "factor", "folder"
valdim the dimension attribute for the array to be created, which is a vector of lengthone or more giving the maximal indices in each dimension
compress the compression method can be "", "ZIP", "ZIP.fast", "ZIP.default", or "ZIP.max"
closezip if a compression method is specified, get into read mode after compression
add.gdsn 5
Details
name if missing, “Item n” is assigned to name, where n is the number of child nodes + 1.
val if val is list or data.frame, the child node(s) will be added corresponding to objects in listor data.frame.
storage the default value is storage.mode(val), "int" denotes signed integer, "uint" denotes un-signed integer, 8, 16, 24, 32 and 64 denote the number of bits. "bit1" to "bit32" denote the packeddata types for 1 to 32 bits which are packed on disk, and "sbit2" to "sbit32" denote the correspondingsigned integers. "float32" denotes single-precision number, and "float64" denotes double-precisionnumber. "string" represents strings of 8-bit characters, "wstring" represents strings of 16-bit char-acters following UTF16 industry standard, and "dwstring" represents strings of 32-bit charactersfollowing UTF32 industry standard. "folder" is to create a folder.
valdim the values in data are taken to be those in the array with the leftmost subscript movingfastest. Some of entries can be ZERO!
compress Z compression algorithm can be used to deflate the data stored in the GDS file. "ZIP"option is equivalent to "ZIP.default". "ZIP.fast", "ZIP.default" and "ZIP.max" correspond to differentcompression levels. In the comprssion mode, you can not change the non-first dimension and readdata field. Call readmode.gdsn to return read mode.
closezip if compression option is specified, then enter a read mode after deflating the data. seereadmode.gdsn.
Value
An object of class gdsn.class of the added node.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn, name.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))L <- -2500:2499
########################################################################### commom types
add.gdsn(f, "int", val=as.integer(1:10000), compress="ZIP", closezip=TRUE)add.gdsn(f, "int.matrix", val=matrix(L, nrow=100, ncol=50))add.gdsn(f, "double", val=seq(1, 1000, 0.4))
6 addfile.gdsn
add.gdsn(f, "character", val=c("int", "double", "logical", "factor"))add.gdsn(f, "logical", val=rep(c(TRUE, FALSE, NA), 50))add.gdsn(f, "factor", val=as.factor(c(letters, NA, "AA", "CC")))add.gdsn(f, "NA", val=rep(NA, 10))add.gdsn(f, "NaN", val=c(rep(NaN, 20), 1:20))add.gdsn(f, "bit2-matrix", val=matrix(L[1:5000], nrow=50, ncol=100), storage="bit2")# list and data.frameadd.gdsn(f, "list", val=list(X=1:10, Y=seq(1, 10, 0.25)))add.gdsn(f, "data.frame", val=data.frame(X=1:19, Y=seq(1, 10, 0.5)))
########################################################################### save a .RData object
obj <- list(X=1:10, Y=seq(1, 10, 0.1))save(obj, file="tmp.RData")addfile.gdsn(f, "tmp.RData", filename="tmp.RData")
f
read.gdsn(index.gdsn(f, "list"))read.gdsn(index.gdsn(f, "list/Y"))read.gdsn(index.gdsn(f, "data.frame"))
########################################################################### allocate the disk spaces
n1 <- add.gdsn(f, "n1", val=1:100, valdim=c(10, 20))read.gdsn(index.gdsn(f, "n1"))
n2 <- add.gdsn(f, "n2", val=matrix(1:100, 10, 10), valdim=c(15, 20))read.gdsn(index.gdsn(f, "n2"))
closefn.gds(f)
addfile.gdsn Add a GDS node with a file
Description
Adds a GDS node with a file, in a CoreArray Genomic Data Structure (GDS) file.
Usage
addfile.gdsn(node, name, filename, compress=c("ZIP", "ZIP.fast", "ZIP.default", "ZIP.max", ""))
addfile.gdsn 7
Arguments
node an object of class gdsn.class or gds.class: "gdsn" – the node of hierarchicalstructure; "gdsclass" – the root of hieracrchical structure
name the variable name of the added nodefilename the file name of input stream.compress the compression method can be "", "ZIP", "ZIP.fast", "ZIP.default", or "ZIP.max".
Details
name if missing, “Item n” is assigned to name, where n is the number of child nodes + 1.
compress Z compression algorithm can be used to deflate the data stored in the GDS file. "ZIP"option is equivalent to "ZIP.default". "ZIP.fast", "ZIP.default" and "ZIP.max" correspond to differentcompression levels. In the comprssion mode, you can not change the non-first dimension and readdata field. Call readmode.gdsn to return read mode.
Value
An object of class gdsn.class of the added node.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn, name.gdsn, add.gdsn, getfile.gdsn
Examples
# save a .RData objectobj <- list(X=1:10, Y=seq(1, 10, 0.1))save(obj, file="tmp.RData")
# cteate a GDS file "test.gds"f <- createfn.gds("test.gds")
add.gdsn(f, "double", val=seq(1, 1000, 0.4))addfile.gdsn(f, "tmp.RData", "tmp.RData")
f
getfile.gdsn(index.gdsn(f, "tmp.RData"), "tmp1.RData")(obj <- get(load("tmp1.RData")))
# open the GDS fileclosefn.gds(f)
8 append.gdsn
append.gdsn Append data to a specified variable
Description
Appends data to the data field of a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
append.gdsn(node, val, check = TRUE)
Arguments
node an object of class gdsn.class, a GDS node
val data to be appended
check whether a warning is given, when appended data can not match the capability ofdata field
Details
storage.mode(val) should be "integer", "double", "character", or "logical".
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
read.gdsn, write.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
# commom typesn <- add.gdsn(f, "int", val=matrix(as.integer(1:10000), nrow=100, ncol=100),
compress="ZIP")
# no warning, and add a new column
apply.gdsn 9
append.gdsn(n, -1:-100)f
# a warningappend.gdsn(n, -1:-50)f
# no warning here, and add a new columnappend.gdsn(n, -51:-100)f
# you should call "readmode.gdsn", before readingreadmode.gdsn(n)
# check the last columnread.gdsn(n, start=c(1, 102), count=c(-1, 1))
# close the gds fileclosefn.gds(f)
apply.gdsn Apply functions over margins
Description
Returns a vector or list of values obtained by applying a function to margins of a matrix or array, ina CoreArray Genomic Data Structure (GDS) file.
Usage
apply.gdsn(node, margin, FUN, selection=NULL,as.is = c("list", "integer", "double", "character", "none"), ...)
Arguments
node an object of class gdsn.class, or a list of objects of class gdsn.class
margin an integer giving the subscripts which the function will be applied over. E.g.,for a matrix 1 indicates rows, 2 indicates columns
FUN the function to be applied
selection a list or NULL; if a list, it is a list of logical vectors according to dimensionsindicating selection; if NULL, uses all data
as.is returned value: a list, an integer vector, etc
... optional arguments to FUN
Details
The algorithm is optimized by blocking the computations to exploit the high-speed memory insteadof disk.
10 apply.gdsn
Value
A vector or list of values.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
read.gdsn, readex.gdsn, clusterApply.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
(n <- add.gdsn(f, "matrix", val=matrix(1:(10*6), nrow=10)))read.gdsn(index.gdsn(f, "matrix"))
# Apply functions over rows of matrixtmp <- apply.gdsn(n, margin=1, FUN=function(x) print(x))tmp <- apply.gdsn(n, margin=1,selection = list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)),FUN=function(x) print(x))
# Apply functions over columns of matrixtmp <- apply.gdsn(n, margin=2, FUN=function(x) print(x))tmp <- apply.gdsn(n, margin=2,selection = list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)),FUN=function(x) print(x))
# closeclosefn.gds(f)
########################################################## Multiple variables#
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
X <- matrix(1:50, nrow=10)Y <- matrix((1:50)/100, nrow=10)Z1 <- factor(c(rep(c("ABC", "DEF", "ETD"), 3), "TTT"))Z2 <- c(TRUE, FALSE, TRUE, FALSE, TRUE)
assign.gdsn 11
node.X <- add.gdsn(f, "X", X)node.Y <- add.gdsn(f, "Y", Y)node.Z1 <- add.gdsn(f, "Z1", Z1)node.Z2 <- add.gdsn(f, "Z2", Z2)
v <- apply.gdsn(list(X=node.X, Y=node.Y, Z=node.Z1), margin=c(1, 1, 1),FUN=function(x) { print(x) }, as.is="none")
v <- apply.gdsn(list(X=node.X, Y=node.Y, Z=node.Z2), margin=c(2, 2, 1),FUN=function(x) print(x))
# with selection
s1 <- rep(c(FALSE, TRUE), 5)s2 <- c(TRUE, FALSE, TRUE, FALSE, TRUE)
v <- apply.gdsn(list(X=node.X, Y=node.Y, Z=node.Z1), margin=c(1, 1, 1),selection = list(list(s1, s2), list(s1, s2), list(s1)),FUN=function(x) print(x))
v <- apply.gdsn(list(X=node.X, Y=node.Y, Z=node.Z2), margin=c(2, 2, 1),selection = list(list(s1, s2), list(s1, s2), list(s2)),FUN=function(x) print(x))
# closeclosefn.gds(f)
assign.gdsn Assign/append data to a GDS node
Description
Assign data to a GDS node, or append data to a GDS node
Usage
assign.gdsn(dest.obj, src.obj, append)
Arguments
dest.obj an object of class gdsn.class, a destination GDS nodesrc.obj an object of class gdsn.class, a source GDS nodeappend if TRUE, append data; otherwise, replace the old one
Author(s)
Xiuwen Zheng <[email protected]>
12 cleanup.gds
References
http://sourceforge.net/projects/corearray/
See Also
read.gdsn, write.gdsn
cleanup.gds Clean up fragments
Description
Cleans up the fragments of a CoreArray Genomic Data Structure (GDS) file.
Usage
cleanup.gds(fn, deep=FALSE, verbose=TRUE)
Arguments
fn the file name of a GDS file to be opened
deep if TRUE, performs a deep-construction strategy; otherwise, performs fast con-struction
verbose if TRUE, show information
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
openfn.gds, createfn.gds, closefn.gds
closefn.gds 13
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
# commom typesadd.gdsn(f, "int", val=as.integer(1:10000))L <- -2500:2499add.gdsn(f, "int.matrix", val=matrix(L, nrow=100, ncol=50))
# save a .RData objectobj <- list(X=1:10, Y=seq(1, 10, 0.1))save(obj, file="tmp.RData")addfile.gdsn(f, "tmp.RData", filename="tmp.RData")
f
closefn.gds(f)
# clean up fragmentscleanup.gds("test.gds")
# cteate the GDS file "test.gds"(f <- openfn.gds("test.gds"))closefn.gds(f)
closefn.gds Close a GDS file
Description
Closes an open CoreArray Genomic Data Structure (GDS) file.
Usage
closefn.gds(gds)
Arguments
gds an object of class gds.class, returned by createfn.gds or openfn.gds
Details
For better performance, Data in a GDS file are usually cached in memory. Keep in mind that thenew file may not actually be written to disk, until closefn.gds or sync.gds is called. Anyway,when R shuts down, all GDS files created or opened would be automatically closed.
Value
None.
14 clusterApply.gdsn
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
createfn.gds, openfn.gds, sync.gds
clusterApply.gdsn Apply functions over matrix margins in parallel
Description
Returns a vector or list of values obtained by applying a function to margins of a matrix in parallel,in a CoreArray Genomic Data Structure (GDS) file.
Usage
clusterApply.gdsn(cl, gds.fn, node.name, margin, FUN, selection=NULL,as.is = c("list", "integer", "double", "character", "none"), ...)
Arguments
cl a cluster object, created by this package or by the package parallel or snow
gds.fn the file name of a GDS file
node.name a character vector indicating GDS node path
margin an integer giving the subscripts which the function will be applied over. E.g.,for a matrix 1 indicates rows, 2 indicates columns
FUN the function to be applied
selection a list or NULL; if a list, it is a list of logical vectors according to dimensionsindicating selection; if NULL, uses all data
as.is returned value: a list, an integer vector, etc
... optional arguments to FUN
Details
The algorithm of applying is optimized by blocking the computations to exploit the high-speedmemory instead of disk.
Value
A vector or list of values.
clusterApply.gdsn 15
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
apply.gdsn
Examples
############################################################ prepare a GDS file
# cteate the GDS file "test1.gds"f <- createfn.gds("test1.gds")
(n <- add.gdsn(f, "matrix", val=matrix(1:(10*6), nrow=10)))read.gdsn(index.gdsn(f, "matrix"))
closefn.gds(f)
# cteate the GDS file "test2.gds"(f <- createfn.gds("test2.gds"))
X <- matrix(1:50, nrow=10)Y <- matrix((1:50)/100, nrow=10)Z1 <- factor(c(rep(c("ABC", "DEF", "ETD"), 3), "TTT"))Z2 <- c(TRUE, FALSE, TRUE, FALSE, TRUE)
node.X <- add.gdsn(f, "X", X)node.Y <- add.gdsn(f, "Y", Y)node.Z1 <- add.gdsn(f, "Z1", Z1)node.Z2 <- add.gdsn(f, "Z2", Z2)f
closefn.gds(f)
############################################################ apply in parallel
library(parallel)
# Use option cl.core to choose an appropriate cluster size.cl <- makeCluster(getOption("cl.cores", 2))
16 cnt.gdsn
# Apply functions over rows or columns of matrix
clusterApply.gdsn(cl, "test1.gds", "matrix", margin=1, FUN=function(x) x)
clusterApply.gdsn(cl, "test1.gds", "matrix", margin=2, FUN=function(x) x)
clusterApply.gdsn(cl, "test1.gds", "matrix", margin=1,selection = list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)),FUN=function(x) x)
clusterApply.gdsn(cl, "test1.gds", "matrix", margin=2,selection = list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)),FUN=function(x) x)
# Apply functions over rows or columns of multiple data sets
clusterApply.gdsn(cl, "test2.gds", c("X", "Y", "Z1"), margin=c(1, 1, 1),FUN=function(x) x)
# with variable namesclusterApply.gdsn(cl, "test2.gds", c(X="X", Y="Y", Z="Z2"), margin=c(2, 2, 1),FUN=function(x) x)
cnt.gdsn Return the number of child nodes
Description
Returns the number of child nodes for a specified node, in a CoreArray Genomic Data Structure(GDS) file.
Usage
cnt.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Value
The number of child nodes.
Author(s)
Xiuwen Zheng <[email protected]>
compression.gdsn 17
References
http://sourceforge.net/projects/corearray/
See Also
objdesp.gdsn, ls.gdsn, index.gdsn, delete.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds(fn="test.gds")
# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))cnt.gdsn(node)# 3
closefn.gds(f)
compression.gdsn Modify compression mode
Description
Modifies the data compression mode of data field, in a CoreArray Genomic Data Structure (GDS)file.
Usage
compression.gdsn(node, compress = c("", "ZIP", "ZIP.fast", "ZIP.default", "ZIP.max"))
Arguments
node an object of class gdsn.class, a GDS node
compress specify the compression method
Details
Z compression algorithm can be used to deflate the data stored in the GDS file. "ZIP" option isequivalent to "ZIP.default". "ZIP.fast", "ZIP.default" and "ZIP.max" correspond to different com-pression levels.
Value
Return node.
Author(s)
Xiuwen Zheng <[email protected]>
18 createfn.gds
References
http://sourceforge.net/projects/corearray/, http://zlib.net/
See Also
readmode.gdsn, add.gdsn
createfn.gds Create a GDS file
Description
Creates a new CoreArray Genomic Data Structure (GDS) file.
Usage
createfn.gds(fn)
Arguments
fn the file name of a new GDS file to be created
Details
Keep in mind that the new file may not actually be written to disk until closefn.gds or sync.gdsis called.
Value
Return an object of class gds.class:
filename the file name to be created.
id ID of GDS file, internal use.
root an object of class gdsn.class, the root of hierachical structure.
readonly whether it is read-only or not
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
openfn.gds, closefn.gds
delete.attr.gdsn 19
Examples
# cteate the GDS file "test.gds"f <- createfn.gds(fn="test.gds")
# add a list to "test.gds"node <- add.gdsn(f, val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))
closefn.gds(f)
delete.attr.gdsn Delete an attribute
Description
Removes an attribute of a GDS node.
Usage
delete.attr.gdsn(node, name)
Arguments
node an object of class gdsn.class, a GDS node
name the name of an attribute
Details
If there is not an attribute with name, a warning will be given.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
put.attr.gdsn, get.attr.gdsn
20 delete.gdsn
delete.gdsn Delete a GDS node
Description
Deletes a specified node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
delete.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn, name.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds(fn="test.gds")
# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))f
# delete "node"delete.gdsn(node)
closefn.gds(f)
gds.class 21
gds.class the class of GDS file
Description
The class of a GDS file, and its instance is returned from openfn.gds or createfn.gds.
Value
There are three components:
filename the file name to be created.id ID of GDS file, internal use.root an object of class gdsn.class, the root of hierachical structure.readonly whether it is read-only or not
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
createfn.gds, openfn.gds, closefn.gds
gdsn.class the class of a node of GDS file
Description
The class of the node of hierarchical structure from a GDS file, and its instance is returned fromadd.gdsn or index.gdsn.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
createfn.gds, closefn.gds
22 get.attr.gdsn
gdsUnitTest Unit testing
Description
Run the test R codes in the folder of ’unitTests’
Usage
gdsUnitTest()
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
get.attr.gdsn Get attributes
Description
Gets the attributes of a CoreArray GDS node.
Usage
get.attr.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Value
A list of attributes.
Author(s)
Xiuwen Zheng <[email protected]>
getfile.gdsn 23
References
http://sourceforge.net/projects/corearray/
See Also
put.attr.gdsn, delete.attr.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
node <- add.gdsn(f, "int", val=as.integer(1:10000))put.attr.gdsn(node, "missing.value", 10000)
fget.attr.gdsn(node)
closefn.gds(f)
getfile.gdsn Output a file from a stream container
Description
Gets a file from a stream container, in a CoreArray Genomic Data Structure (GDS) file.
Usage
getfile.gdsn(node, out.filename)
Arguments
node an object of class gdsn.class or gds.class: "gdsn" – the node of hierarchicalstructure; "gdsclass" – the root of hieracrchical structure
out.filename the file name of output stream
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
24 index.gdsn
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn, name.gdsn, add.gdsn, addfile.gdsn
Examples
# save a .RData objectobj <- list(X=1:10, Y=seq(1, 10, 0.1))save(obj, file="tmp.RData")
# cteate a GDS file "test.gds"f <- createfn.gds("test.gds")
add.gdsn(f, "double", val=seq(1, 1000, 0.4))addfile.gdsn(f, "tmp.RData", "tmp.RData")
f
getfile.gdsn(index.gdsn(f, "tmp.RData"), "tmp1.RData")(obj <- get(load("tmp1.RData")))
# open the GDS fileclosefn.gds(f)
index.gdsn Return the specified node
Description
Returns a specified node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
index.gdsn(node, path=NULL, index=NULL, silent=FALSE)
Arguments
node an object of class gdsn.class or gds.class: "gdsn" – the node of hierarchicalstructure; "gdsclass" – the root of hieracrchical structure
path the path specifying a GDS node with ’/’ as a separator
index a vector of integers or characters, specifying the path; it has effects when pathis missing
silent if TRUE, return NULL if the specified path does not exist
Details
If index is a vector of integers, e.g., c(1, 2), the result is the second child node of the first childof node. If index is a vector of characters, e.g., c("list", "x"), the result is the child node withname "x" of the "list" child node.
lasterr.gds 25
Value
An object of class gdsn.class for the specified node.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, name.gdsn, delete.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds(fn="test.gds")
# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))f
index.gdsn(f, "list/x")index.gdsn(f, index=c("list", "x"))index.gdsn(f, index=c(1, 1))
index.gdsn(f, index=c("list", "z"))
closefn.gds(f)
lasterr.gds Return the last error
Description
Gets the last error of gdsfmt.
Usage
lasterr.gds()
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
26 ls.gdsn
ls.gdsn Return the names of child nodes
Description
Gets a list of names for its child nodes, in a CoreArray Genomic Data Structure (GDS) file.
Usage
ls.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Value
A vector of characters.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds("test.gds")
# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))
ls.gdsn(node)
closefn.gds(f)
name.gdsn 27
name.gdsn Return the variable name of a node
Description
Gets the variable name of a node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
name.gdsn(node, fullname = FALSE)
Arguments
node an object of class gdsn.class, a GDS node
fullname if FALSE, return the node name (by default), otherwise the full name
Value
A vector of charactors.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, rename.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds("test.gds")
# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))
name.gdsn(node)# "list"
name.gdsn(node, fullname=TRUE)# "test/list"
closefn.gds(f)
28 objdesp.gdsn
objdesp.gdsn Get node description
Description
Gets the descritpion of a specified node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
objdesp.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Value
Returns a list:
type the description of data field
name the variable name of a specified node
svtype the internal type of the specified node: 1 – Int8, 2 – UInt8, 3 – Int16, 4 – UInt16,5 – Int32, 6 – UInt32, 7 – Int64, 8 – UInt64, 9 – Int128, 10 – UInt128, 11 –Float32, 12 – Float64, 13 – Long Float, 14 – UTF8 String, 15 – UTF16 String,16 – UTF32 String, 0 – others
is.array indicates whether it is array-type
dim the dimension of data field
compress the compression method: "", "ZIP", etc
cpratio data compression ratio, "NaN" indicates no compression
maxlen if svtype = 14, 15 or 16, it is the maximum length of characters
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, name.gdsn, ls.gdsn, index.gdsn, delete.gdsn, add.gdsn
openfn.gds 29
Examples
# cteate the GDS file "test.gds"f <- createfn.gds("test.gds")
# add a vector to "test.gds"node1 <- add.gdsn(f, name="vector1", val=1:10000, compress="ZIP")objdesp.gdsn(node1)
# add a character to "test.gds"node2 <- add.gdsn(f, name="vector2", val=c("A", "BC", "DEF"), compress="ZIP")objdesp.gdsn(node2)
closefn.gds(f)
openfn.gds Open a GDS file
Description
Opens an existing file of CoreArray Genomic Data Structure (GDS) for reading or writing.
Usage
openfn.gds(fn, readonly = TRUE)
Arguments
fn the file name of a GDS file to be opened
readonly if TRUE, the file is opened read-only; otherwise, writing to the file is allowed.
Details
This routine opens an existing GDS file for reading (or, if readonly=FALSE, for writing). To createa new GDS file, use createfn.gds instead.
If the file is opened read-only, all data in the file are not allowed to change, including hierachicalstructure, variable names, data field, etc.
Value
Return an object of class gds.class.
filename the file name
id ID of GDS file, internal use
root an object of class gdsn.class, the root of hierachical structure
readonly whether it is read-only or not
30 print.gds.class
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
createfn.gds, closefn.gds
Examples
# cteate the GDS file "test.gds"f <- createfn.gds("test.gds")# add a list to "test.gds"node <- add.gdsn(f, name="list", val=list(x=c(1,2), y=c("T", "B", "C"), z=TRUE))# closeclosefn.gds(f)
# openf <- openfn.gds("test.gds")# read(node <- index.gdsn(f, "list"))read.gdsn(node)# closeclosefn.gds(f)
print.gds.class Show the information of class "gds.class"
Description
Displays an object of class "gds.class", in a CoreArray Genomic Data Structure (GDS) file.
Usage
## S3 method for class ’gds.class’print(x, all=FALSE, ...)
Arguments
x an object of class gds.class, a CoreArray GDS file
all if FALSE, hide GDS nodes with an attribute "R.invisible"
... the arguments passed to or from other methods
Author(s)
Xiuwen Zheng <[email protected]>
print.gdsn.class 31
References
http://sourceforge.net/projects/corearray/
See Also
print.gdsn.class
print.gdsn.class Show the information of class "gdsn.class"
Description
Displays an object of class "gdsn.class", a GDS node in a CoreArray Genomic Data Structure (GDS)file.
Usage
## S3 method for class ’gdsn.class’print(x, expand = TRUE, all=FALSE, ...)
Arguments
x an object of class gdsn.class, a GDS node
expand whether enumerate all of child nodes
all if FALSE, hide GDS nodes with an attribute "R.invisible"
... the arguments passed to or from other methods
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
print.gds.class
32 put.attr.gdsn
put.attr.gdsn Add an attribute into a GDS file
Description
Adds an attribute to a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
put.attr.gdsn(node, name, val = NULL)
Arguments
node an object of class gdsn.class, a GDS node
name the name of an attribute
val the value of an attribute
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
get.attr.gdsn, delete.attr.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
node <- add.gdsn(f, "int", val=as.integer(1:10000))put.attr.gdsn(node, "missing.value", 10000)
fget.attr.gdsn(node)
closefn.gds(f)
read.gdsn 33
read.gdsn Read data field of a GDS node
Description
Gets data from a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
read.gdsn(node, start, count)
Arguments
node an object of class gdsn.class, a GDS node
start a vector of integers, starting from 1 for each dimension component
count a vector of integers, the length of each dimnension. As a special case, the value"-1" indicates that all entries along that dimension should be written
Details
start, count: the values in data are taken to be those in the array with the leftmost subscriptmoving fastest.
Value
Returns an array, list, or data.frame.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
readex.gdsn, append.gdsn, write.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
add.gdsn(f, "vector", val=1:128)add.gdsn(f, "list", val=list(X=1:10, Y=seq(1, 10, 0.25)))add.gdsn(f, "data.frame", val=data.frame(X=1:19, Y=seq(1, 10, 0.5)))
34 readex.gdsn
f
read.gdsn(index.gdsn(f, "vector"))read.gdsn(index.gdsn(f, "list"))read.gdsn(index.gdsn(f, "data.frame"))
closefn.gds(f)
readex.gdsn Read data field of a GDS node with a selection
Description
Gets data from a GDS node with subset selection, in a CoreArray Genomic Data Structure (GDS)file.
Usage
readex.gdsn(node, sel=NULL)
Arguments
node an object of class gdsn.class, the GDS node
sel a list of m logical vectors, where m is the number of dimensions of node andeach logical vector should have the same size of dimension in node
Value
Return an array.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
read.gdsn, append.gdsn, write.gdsn, add.gdsn
readmode.gdsn 35
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
add.gdsn(f, "vector", val=1:128)add.gdsn(f, "matrix", val=matrix(as.character(1:(10*6)), nrow=10))f
# read vectorreadex.gdsn(index.gdsn(f, "vector"), sel=rep(c(TRUE, FALSE), 64))
# read matrixreadex.gdsn(index.gdsn(f, "matrix"))readex.gdsn(index.gdsn(f, "matrix"),sel=list(d1=rep(c(TRUE, FALSE), 5), d2=rep(c(TRUE, FALSE), 3)))
closefn.gds(f)
readmode.gdsn Get into read mode in the compression mode
Description
Gets into the read mode for a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
readmode.gdsn(node)
Arguments
node an object of class gdsn.class, a GDS node
Details
After the compressed data field is created, it is in writing mode. Users can add new data to thecompressed data field, but can not read data from the data field. Users need to call readmode.gdsnfor reading.
Once get into the read mode, users can not add more data to the data field. If users would like toappend more data or modify the data field, please call compression.gdsn (node, compress="")to decompress data first.
Value
Return node.
Author(s)
Xiuwen Zheng <[email protected]>
36 rename.gdsn
References
http://sourceforge.net/projects/corearray/
See Also
compression.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))
# commom typesn <- add.gdsn(f, "int", val=as.integer(1:10000), compress="ZIP")
# you can not read "int", because "int" is in writing mode.# read.gdsn(n)
readmode.gdsn(n)
# now you can read "int"read.gdsn(n)
closefn.gds(f)
rename.gdsn Rename a GDS node
Description
Renames a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
rename.gdsn(node, newname)
Arguments
node an object of class gdsn.class, a GDS node
newname the new name of a specified node
Details
CoreArray hierarchical structure does not allow duplicate names in the same path.
Value
Returns node.
setdim.gdsn 37
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
cnt.gdsn, objdesp.gdsn, ls.gdsn, index.gdsn
Examples
# cteate the GDS file "test.gds"f <- createfn.gds("test.gds")n <- add.gdsn(f, "old.name", val=1:10)f
rename.gdsn(n, "new.name")f
closefn.gds(f)
setdim.gdsn Set the dimension of data field
Description
Assigns a new dimension to the data field of a GDS node, in a CoreArray Genomic Data Structure(GDS) file.
Usage
setdim.gdsn(node, valdim)
Arguments
node an object of class gdsn.class, a GDS node
valdim the new dimension for the array to be created, which is a vector of length one ormore giving the maximal indices in each dimension
Value
Returns node.
Author(s)
Xiuwen Zheng <[email protected]>
38 sync.gds
References
http://sourceforge.net/projects/corearray/
See Also
read.gdsn, write.gdsn, append.gdsn, add.gdsn
Examples
# cteate the GDS file "test.gds"(f <- createfn.gds("test.gds"))n <- add.gdsn(f, "int", val=as.integer(1:100))fsetdim.gdsn(n, c(120, 4))fclosefn.gds(f)
sync.gds Synchronize a GDS file
Description
Writes the data cached in memory to disk.
Usage
sync.gds(gds)
Arguments
gds An object of class gds.class, returned by createfn.gds or openfn.gds
Details
For better performance, Data in a GDS file are usually cached in memory. Keep in mind that thenew file may not actually be written to disk, until closefn.gds or sync.gds is called. Anyway,when R shuts down, all GDS files created or opened would be automatically closed.
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
write.gdsn 39
See Also
createfn.gds, openfn.gds
write.gdsn Write data to a GDS node
Description
Writes data to a GDS node, in a CoreArray Genomic Data Structure (GDS) file.
Usage
write.gdsn(node, val, start, count)
Arguments
node an object of class gdsn.class, a GDS node
val the data to be written
start a vector of integers, starting from 1 for each dimension
count a vector of integers, the length of each dimnension
Details
start, count: The values in data are taken to be those in the array with the leftmost subscriptmoving fastest.
start and count should both exist or be missing. If start and count are both missing, the dimen-sions and values of val will be assigned to the data field.
Value
None.
Author(s)
Xiuwen Zheng <[email protected]>
References
http://sourceforge.net/projects/corearray/
See Also
append.gdsn, read.gdsn, add.gdsn
40 write.gdsn
Examples
(f <- createfn.gds("test.gds"))L <- -2500:2499
# commom typesadd.gdsn(f, "int.matrix", val=matrix(L, nrow=100, ncol=50),
valdim=c(110, 60))write.gdsn(index.gdsn(f, "int.matrix"), val=rep(0, 100), start=c(20, 20),
count=c(10, 10))fclosefn.gds(f)
Index
∗Topic GDSadd.gdsn, 4addfile.gdsn, 6append.gdsn, 8apply.gdsn, 9assign.gdsn, 11cleanup.gds, 12closefn.gds, 13clusterApply.gdsn, 14cnt.gdsn, 16compression.gdsn, 17createfn.gds, 18delete.attr.gdsn, 19delete.gdsn, 20gds.class, 21gdsfmt-package, 2gdsn.class, 21gdsUnitTest, 22get.attr.gdsn, 22getfile.gdsn, 23index.gdsn, 24lasterr.gds, 25ls.gdsn, 26name.gdsn, 27objdesp.gdsn, 28openfn.gds, 29print.gds.class, 30print.gdsn.class, 31put.attr.gdsn, 32read.gdsn, 33readex.gdsn, 34readmode.gdsn, 35rename.gdsn, 36setdim.gdsn, 37sync.gds, 38write.gdsn, 39
∗Topic IOgdsfmt-package, 2
∗Topic database
gdsfmt-package, 2∗Topic file
gdsfmt-package, 2∗Topic interface
gdsfmt-package, 2∗Topic utilities
add.gdsn, 4addfile.gdsn, 6append.gdsn, 8apply.gdsn, 9assign.gdsn, 11cleanup.gds, 12closefn.gds, 13clusterApply.gdsn, 14cnt.gdsn, 16compression.gdsn, 17createfn.gds, 18delete.attr.gdsn, 19delete.gdsn, 20gds.class, 21gdsfmt-package, 2gdsn.class, 21gdsUnitTest, 22get.attr.gdsn, 22getfile.gdsn, 23index.gdsn, 24lasterr.gds, 25ls.gdsn, 26name.gdsn, 27objdesp.gdsn, 28openfn.gds, 29print.gds.class, 30print.gdsn.class, 31put.attr.gdsn, 32read.gdsn, 33readex.gdsn, 34readmode.gdsn, 35rename.gdsn, 36setdim.gdsn, 37
41
42 INDEX
sync.gds, 38write.gdsn, 39
add.gdsn, 4, 7, 8, 17, 18, 20, 21, 24, 25, 28,33, 34, 36, 38, 39
addfile.gdsn, 6, 24append.gdsn, 8, 33, 34, 38, 39apply.gdsn, 9, 15assign.gdsn, 11
cleanup.gds, 12closefn.gds, 12, 13, 13, 18, 21, 30, 38clusterApply.gdsn, 10, 14cnt.gdsn, 5, 7, 16, 20, 24–28, 37compression.gdsn, 17, 35, 36createfn.gds, 12–14, 18, 21, 29, 30, 38, 39
delete.attr.gdsn, 19, 23, 32delete.gdsn, 17, 20, 25, 28
gds.class, 4, 7, 13, 18, 21, 23, 24, 29, 30, 38gdsfmt (gdsfmt-package), 2gdsfmt-package, 2gdsn.class, 4, 5, 7–9, 11, 16–21, 21, 22–29,
31–37, 39gdsUnitTest, 22get.attr.gdsn, 19, 22, 32getfile.gdsn, 7, 23
index.gdsn, 5, 7, 17, 20, 21, 24, 24, 26, 28, 37
lasterr.gds, 25ls.gdsn, 5, 7, 17, 20, 24–26, 26, 27, 28, 37
name.gdsn, 5, 7, 20, 24, 25, 27, 28
objdesp.gdsn, 5, 7, 17, 20, 24–27, 28, 37openfn.gds, 12–14, 18, 21, 29, 38, 39
parallel, 14print.gds.class, 30, 31print.gdsn.class, 31, 31put.attr.gdsn, 19, 23, 32
read.gdsn, 8, 10, 12, 33, 34, 38, 39readex.gdsn, 10, 33, 34readmode.gdsn, 5, 7, 18, 35rename.gdsn, 27, 36
setdim.gdsn, 37sync.gds, 13, 14, 18, 38, 38
write.gdsn, 8, 12, 33, 34, 38, 39