seqAddValue: Add values to a GDS File

In zhengxwen/SeqArray: Data Management of Large-Scale Whole-Genome Sequence Variant Calls

Add values to a GDS File

Description

Add or modify the values in a GDS file with hash code

Usage

seqAddValue(gdsfile, varnm, val, desp=character(), replace=FALSE,
    compress="LZMA_RA", packed=TRUE, packed.idx=TRUE, verbose=TRUE,
    verbose.attr=TRUE)

Arguments

gdsfile	character for file name, or a SeqVarGDSClass object
varnm	the variable name, e.g., "sample.id", "variant.id", "chromosome", "annotation/info/NEW_VARIABLE"
val	the R value can be integers, real numbers, characters, factor, logical, raw variable, data.frame or a list; a list of vectors is used for variable-length annotation data; or NULL for adding a new folder
desp	variable description
replace	if TRUE, replace the existing variable silently if possible
compress	the compression method can be "" (no compression), see add.gdsn
packed	TRUE, pack data if there is any missing value
packed.idx	TRUE, store the index variable using integers with the fewest bits if possible
verbose	if TRUE, show information
verbose.attr	if TRUE, show attribute information in a GDS node

Value

Return none.

Author(s)

Xiuwen Zheng

See Also

seqVCF2GDS, seqNewVarData

Examples

# the file of GDS
gds.fn <- seqExampleFileName("gds")
file.copy(gds.fn, "tmp.gds", overwrite=TRUE)

# display
(f <- seqOpen("tmp.gds", readonly=FALSE))

show(index.gdsn(f, "sample.id"))
seqAddValue(f, "sample.id", 1:90, replace=TRUE)
show(index.gdsn(f, "sample.id"))

show(index.gdsn(f, "chromosome"))
v <- seqGetData(f, "chromosome")
seqAddValue(f, "chromosome", paste0("chr", v), replace=TRUE)
show(index.gdsn(f, "chromosome"))
table(seqGetData(f, "chromosome"))

# annotation info
seqAddValue(f, "annotation/info/folder", NULL)  # add a new folder
seqAddValue(f, "annotation/info/folder/val", 1:1348, "random number")
seqAddValue(f, "annotation/info/folder/packed", c(rep(2L, 1000), rep(NA, 348)))
seqAddValue(f, "annotation/info/newff",
    data.frame(x=1:1348, y=rep("s", 1348), stringsAsFactors=FALSE),
    desp=c("integer numbers", "character"))

# variable-length annotation info data
v <- lapply(1:1348, function(x) as.character(x))
v[[1]] <- 1:10
seqAddValue(f, "annotation/info/folder/val1", v)
head(seqGetData(f, "annotation/info/folder/val1", .tolist=TRUE))


# sample annotation
seqAddValue(f, "sample.annotation", data.frame(ii=1:90, y=rep("A", 90)),
    replace=TRUE)
seqAddValue(f, "sample.annotation/float", (1:90)/90)

# close the GDS file
seqClose(f)


# remove the temporary file
unlink("tmp.gds", force=TRUE)

zhengxwen/SeqArray documentation built on May 1, 2024, 6:26 p.m.