readex.gdsn: Read data field of a GDS node with a selection

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

Description

Get data from a GDS node with subset selection.

Usage

readex.gdsn(node, sel=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
sel	a list of m logical vectors, where m is the number of dimensions of node and each logical vector should have the same size of dimension in node
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

If sel is a list of numeric vectors, the internal method converts the numeric vectors to logical vectors first, extract data with logical vectors, and then call [ to reorder or expend data.

Value

Return an array.

Author(s)

Xiuwen Zheng

References

http://github.com/zhengxwen/gdsfmt

See Also

read.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, "matrix", matrix(as.character(1:(10*6)), nrow=10))
f

# read vector
readex.gdsn(index.gdsn(f, "vector"), sel=rep(c(TRUE, FALSE), 64))
readex.gdsn(index.gdsn(f, "vector"), sel=c(4:8, 1, 2, 12))
readex.gdsn(index.gdsn(f, "vector"), sel=-1:-10)

readex.gdsn(index.gdsn(f, "vector"), sel=c(4, 1, 10, NA, 12, NA))
readex.gdsn(index.gdsn(f, "vector"), sel=c(4, 1, 10, NA, 12, NA),
    .value=c(NA, 1, 12), .substitute=c(6, 7, NA))


# read matrix
readex.gdsn(index.gdsn(f, "matrix"))
readex.gdsn(index.gdsn(f, "matrix"),
    sel=list(rep(c(TRUE, FALSE), 5), rep(c(TRUE, FALSE), 3)))
readex.gdsn(index.gdsn(f, "matrix"), sel=list(NULL, c(1,3,6)))
readex.gdsn(index.gdsn(f, "matrix"),
    sel=list(rep(c(TRUE, FALSE), 5), c(1,3,6)))
readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(1,3,6,10), c(1,3,6)))
readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(-1,-3), -6))

readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(1,3,NA,10), c(1,3,NA,5)))
readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(1,3,NA,10), c(1,3,NA,5)),
    simplify="force")

readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(1,3,NA,10), c(1,3,NA,5)))
readex.gdsn(index.gdsn(f, "matrix"), sel=list(c(1,3,NA,10), c(1,3,NA,5)),
    .value=NA, .substitute="X")


# close the GDS file
closefn.gds(f)


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

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