seqGetFilter {SeqArray} | R Documentation

## Get the Filter of GDS File

### Description

Gets the filter of samples and variants.

### Usage

    seqGetFilter(gdsfile, .useraw=FALSE)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object
`.useraw` | returns logical vectors if `FALSE`, and returns raw vectors if `TRUE`

### Value

Return a list:

`sample.sel` | a logical/raw vector indicating selected samples
`variant.sel` | a logical/raw vector indicating selected variants

### Author(s)

Xiuwen Zheng

### See Also

`seqSetFilter`

### Examples

    # the GDS file
    (gds.fn <- seqExampleFileName("gds"))

    # display
    (f <- seqOpen(gds.fn))

    # get 'sample.id
    (samp.id <- seqGetData(f, "sample.id"))
    # "NA06984" "NA06985" "NA06986" ...

    # get 'variant.id'
    head(variant.id <- seqGetData(f, "variant.id"))

    # set sample and variant filters
    seqSetFilter(f, sample.id=samp.id[c(2,4,6,8,10)])
    set.seed(100)
    seqSetFilter(f, variant.id=sample(variant.id, 10))

    # get filter
    z <- seqGetFilter(f)

    # the number of selected samples
    sum(z$sample.sel)
    # the number of selected variants
    sum(z$variant.sel)

    z <- seqGetFilter(f, .useraw=TRUE)
    head(z$sample.sel)
    head(z$variant.sel)

    # close the GDS file
    seqClose(f)

[Package SeqArray version 1.26.2 Index]