gdsfmt (version 1.8.3)

cleanup.gds: Clean up fragments

Description

Clean up the fragments of a CoreArray Genomic Data Structure (GDS) file.

Usage

cleanup.gds(filename, verbose=TRUE)

Arguments

filename

the file name of a GDS file to be opened

verbose

if TRUE, show information

Value

None.

References

http://github.com/zhengxwen/gdsfmt

See Also

openfn.gds, createfn.gds, closefn.gds

Examples

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

# commom types
add.gdsn(f, "int", val=1:10000)
L <- -2500:2499
add.gdsn(f, "int.matrix", val=matrix(L, nrow=100, ncol=50))

# 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

# close the GDS file
closefn.gds(f)


# clean up fragments
cleanup.gds("test.gds")


# open ...
(f <- openfn.gds("test.gds"))
closefn.gds(f)


# delete the temporary file
unlink("test.gds", force=TRUE)