read.gdsn: Read data field of a GDS node
In gdsfmt: R Interface to CoreArray Genomic Data Structure (GDS) Files

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

Get data from a GDS node.

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read.gdsn(node, start=NULL, count=NULL,
    simplify=c("auto", "none", "force"), .useraw=FALSE, .value=NULL,
    .substitute=NULL, .sparse=TRUE)

`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 read, starting from `start`
`simplify`	if `"auto"`, the result is collapsed to be a vector if possible; `"force"`, the result is forced to be a vector
`.useraw`	use R RAW storage mode if integers can be stored in a byte, to reduce memory usage
`.value`	a vector of values to be replaced in the original data array, or NULL for nothing
`.substitute`	a vector of values after replacing, or NULL for nothing; `length(.substitute)` should be one or `length(.value)`; if `length(.substitute)` = `length(.value)`, it is a mapping from `.value` to `.substitute`
`.sparse`	only applicable for the sparse array nodes, if `TRUE` and it is a vector or matrix, return a `Matrix::dgCMatrix` object

start, count: the values in data are taken to be those in the array with the leftmost subscript moving fastest.

Return an array, list, or data.frame.

Xiuwen Zheng

http://github.com/zhengxwen/gdsfmt

readex.gdsn, append.gdsn, write.gdsn, add.gdsn

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

add.gdsn(f, "vector", 1:128)
add.gdsn(f, "list", list(X=1:10, Y=seq(1, 10, 0.25)))
add.gdsn(f, "data.frame", data.frame(X=1:19, Y=seq(1, 10, 0.5)))
add.gdsn(f, "matrix", matrix(1:12, ncol=4))

f

read.gdsn(index.gdsn(f, "vector"))
read.gdsn(index.gdsn(f, "list"))
read.gdsn(index.gdsn(f, "data.frame"))


# the effects of 'simplify'
read.gdsn(index.gdsn(f, "matrix"), start=c(2,2), count=c(-1,1))
# [1] 5 6  <- a vector

read.gdsn(index.gdsn(f, "matrix"), start=c(2,2), count=c(-1,1),
    simplify="none")
#      [,1]  <- a matrix
# [1,]    5
# [2,]    6

read.gdsn(index.gdsn(f, "matrix"), start=c(2,2), count=c(-1,3))
read.gdsn(index.gdsn(f, "matrix"), start=c(2,2), count=c(-1,3),
    .value=c(12,5), .substitute=NA)


# close the GDS file
closefn.gds(f)


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