assign.gdsn: Assign/append data to a GDS node

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

Assign/append data to a GDS node

Description

Assign data to a GDS node, or append data to a GDS node

Usage

assign.gdsn(node, src.node=NULL, resize=TRUE, seldim=NULL, append=FALSE,
    .value=NULL, .substitute=NULL)

Arguments

node	an object of class gdsn.class, a target GDS node
src.node	an object of class gdsn.class, a source GDS node
resize	whether call setdim.gdsn to reset the dimension(s)
seldim	the selection of src.obj with numeric or logical indicators, or NULL for all data
append	if TRUE, append data by calling append.gdsn; otherwise, replace the old one
.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

Value

None.

Author(s)

Xiuwen Zheng

See Also

read.gdsn, readex.gdsn, apply.gdsn, write.gdsn, append.gdsn

Examples

f <- createfn.gds("test.gds")

n1 <- add.gdsn(f, "n1", 1:100)
n2 <- add.gdsn(f, "n2", storage="int", valdim=c(20, 0))
n3 <- add.gdsn(f, "n3", storage="int", valdim=c(0))
n4 <- add.gdsn(f, "n4", matrix(1:48, 6))
f

assign.gdsn(n2, n1, resize=FALSE, append=TRUE)

read.gdsn(n1)
read.gdsn(n2)

assign.gdsn(n2, n1, resize=FALSE, append=TRUE)
append.gdsn(n2, n1)
read.gdsn(n2)

assign.gdsn(n3, n2, seldim=
    list(rep(c(TRUE, FALSE), 10), c(rep(c(TRUE, FALSE), 7), TRUE)))
read.gdsn(n3)

setdim.gdsn(n2, c(25,0))
assign.gdsn(n2, n1, append=TRUE, seldim=rep(c(TRUE, FALSE), 50))
read.gdsn(n2)

assign.gdsn(n2, n1); read.gdsn(n2)
f

##

read.gdsn(n4)

# substitute
assign.gdsn(n4, .value=c(3:8,35:40), .substitute=NA); read.gdsn(n4)

# subset
assign.gdsn(n4, seldim=list(c(4,2,6,NA), c(5,6,NA,2,8,NA,4))); read.gdsn(n4)


n4 <- add.gdsn(f, "n4", matrix(1:48, 6), replace=TRUE)
read.gdsn(n4)
# sort into descending order
assign.gdsn(n4, seldim=list(6:1, 8:1)); read.gdsn(n4)


# close the GDS file
closefn.gds(f)


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

zhengxwen/gdsfmt documentation built on Nov. 19, 2024, 1:03 p.m.