read.gdsn: Read data field of a GDS node

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

Read data field of a GDS node

Description

Get data from a GDS node.

Usage

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

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 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

Details

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

Value

Return an array, list, or data.frame.

Author(s)

Xiuwen Zheng

See Also

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

Examples

# 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)

zhengxwen/gdsfmt documentation built on Sept. 27, 2024, 10:08 a.m.