addfile.gdsn: Add a GDS node with a file
In gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

Description Usage Arguments Details Value Author(s) References See Also Examples

Add a file to a GDS file as a node.

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addfile.gdsn(node, name, filename,
    compress=c("ZIP", "ZIP_RA", "LZMA", "LZMA_RA", "LZ4", "LZ4_RA"),
    replace=FALSE, visible=TRUE)

`node`	an object of class `gdsn.class` or `gds.class`
`name`	the variable name; if it is not specified, a temporary name is assigned
`filename`	the file name of input stream.
`compress`	the compression method can be "" (no compression), "ZIP", "ZIP.fast", "ZIP.default", "ZIP.max" or "ZIP.none" (original zlib); "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or "ZIP_RA.none" (zlib with efficient random access); "LZ4", "LZ4.none", "LZ4.fast", "LZ4.hc" or "LZ4.max"; "LZ4_RA", "LZ4_RA.none", "LZ4_RA.fast", "LZ4_RA.hc" or "LZ4_RA.max" (with efficient random access). See details
`replace`	if `TRUE`, replace the existing variable silently if possible
`visible`	`FALSE` – invisible/hidden, except `print(, all=TRUE)`

compress: Z compression algorithm (http://www.zlib.net/) 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 different compression levels.

To support efficient random access of Z stream, "ZIP_RA", "ZIP_RA.fast", "ZIP_RA.default", "ZIP_RA.max" or "ZIP_RA.none" should be specified. "ZIP_RA" option is equivalent to "ZIP_RA.default:256K". The block size can be specified by following colon, and "16K", "32K", "64K", "128K", "256K", "512K", "1M", "2M", "4M" and "8M" are allowed, like "ZIP_RA:64K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, like 64K.

LZ4 fast lossless compression algorithm is allowed when compress="LZ4" (http://code.google.com/p/lz4/). Three compression levels can be specified, "LZ4.fast" (LZ4 fast mode), "LZ4.hc" (LZ4 high compression mode), "LZ4.max" (maximize the compression ratio). The block size can be specified by following colon, and "64K", "256K", "1M" and "4M" are allowed according to LZ4 frame format. "LZ4" is equivalent to "LZ4.hc:256K".

To support efficient random access of LZ4 stream, "LZ4_RA", "LZ4_RA.fast", "LZ4_RA.hc", "ZIP_RA.max" or "LZ4_RA.none" should be specified. "LZ4_RA" option is equivalent to "LZ4_RA.hc:256K". The block size can be specified by following colon, and "16K", "32K", "64K", "128K", "256K", "512K", "1M", "2M", "4M" and "8M" are allowed, like "LZ4_RA:64K". The compression algorithm tries to keep each independent compressed data block to be about of the specified block size, like 64K.

An object of class gdsn.class.

Xiuwen Zheng

http://github.com/zhengxwen/gdsfmt

getfile.gdsn, add.gdsn

# save a .RData object
obj <- list(X=1:10, Y=seq(1, 10, 0.1))
save(obj, file="tmp.RData")

# cteate a GDS file
f <- createfn.gds("test.gds")

add.gdsn(f, "double", val=seq(1, 1000, 0.4))
addfile.gdsn(f, "tmp.RData", "tmp.RData")

# open the GDS file
closefn.gds(f)


# open the existing file
(f <- openfn.gds("test.gds"))

getfile.gdsn(index.gdsn(f, "tmp.RData"), "tmp1.RData")
(obj <- get(load("tmp1.RData")))

# open the GDS file
closefn.gds(f)


# delete the temporary files
unlink(c("test.gds", "tmp.RData", "tmp1.RData"), force=TRUE)