seqAddValue {SeqArray} | R Documentation

## 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, 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
`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
`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`

### Examples

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

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

[Package SeqArray version 1.28.1 Index]