addfolder.gdsn: Add a folder to the GDS node

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

Description

Add a directory or a virtual folder to the GDS node.

Usage

addfolder.gdsn(node, name, type=c("directory", "virtual"), gds.fn="",
    replace=FALSE, visible=TRUE)

Arguments

node	an object of class gdsn.class or gds.class
name	the variable name; if it is not specified, a temporary name is assigned
type	"directory" (default) – create a directory of GDS node; "virtual" – create a virtual folder linking another GDS file by mapping all of the content to this virtual folder
gds.fn	the name of another GDS file; it is applicable only if type="virtual"
replace	if TRUE, replace the existing variable silently if possible
visible	FALSE – invisible/hidden, except print(, all=TRUE)

Value

An object of class gdsn.class.

Author(s)

Xiuwen Zheng

References

http://github.com/zhengxwen/gdsfmt

See Also

add.gdsn, addfile.gdsn

Examples

# create the first GDS file
f1 <- createfn.gds("test1.gds")

add.gdsn(f1, "NULL")
addfolder.gdsn(f1, "dir")
add.gdsn(f1, "int", 1:100)
f1

# open the GDS file
closefn.gds(f1)

##############################################

# create the second GDS file
f2 <- createfn.gds("test2.gds")

add.gdsn(f2, "int", 101:200)

# link to the first file
addfolder.gdsn(f2, "virtual_folder", type="virtual", gds.fn="test1.gds")

f2

# open the GDS file
closefn.gds(f2)


##############################################

# open the second file (writable)
(f <- openfn.gds("test2.gds", FALSE))
# +    [  ]
# |--+ int   { Int32 100, 400 bytes }
# |--+ virtual_folder   [ --> test1.gds ]
# |  |--+ NULL       
# |  |--+ dir   [  ]
# |  |--+ int   { Int32 100, 400 bytes }

read.gdsn(index.gdsn(f, "int"))
read.gdsn(index.gdsn(f, "virtual_folder/int"))
add.gdsn(index.gdsn(f, "virtual_folder/dir"), "nm", 1:10)

f

# open the GDS file
closefn.gds(f)


##############################################
# open 'test1.gds', there is a new variable "dir/nm"

(f <- openfn.gds("test1.gds"))
closefn.gds(f)


##############################################
# remove 'test1.gds'

file.remove("test1.gds")

## Not run: 
(f <- openfn.gds("test2.gds"))
# +    [  ]
# |--+ int   { Int32 100, 400 bytes }
# |--+ virtual_folder   [ -X- test1.gds ]

closefn.gds(f)
## End(Not run)

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

gdsfmt documentation built on Dec. 26, 2020, 6 p.m.