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="", replace=FALSE, compress="LZMA_RA",
        packed=FALSE)

### Arguments

`gdsfile` | 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 or raw variable, `list` and `data.frame`
`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` | FALSE

### Value

Return none.

### Author(s)

Xiuwen Zheng

### See Also

`seqVCF2GDS`

### Examples

    library(SeqArray)

    # 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"))

    # 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 1.26.2 Index]