gdsSubset {GWASTools} | R Documentation

## Write a subset of data in a GDS file to a new GDS file

### Description

`gdsSubset` takes a subset of data (snps and samples) from a GDS file and write it to a new GDS file. `gdsSubsetCheck` checks that a GDS file is the desired subset of another GDS file.

### Usage

    gdsSubset(parent.gds, sub.gds,
              sample.include=NULL, snp.include=NULL,
              sub.storage=NULL,
              compress="LZMA_RA",
              block.size=5000,
              verbose=TRUE)

    gdsSubsetCheck(parent.gds, sub.gds,
                   sample.include=NULL, snp.include=NULL,
                   sub.storage=NULL,
                   verbose=TRUE)

### Arguments

`parent.gds` | Name of the parent GDS file
`sub.gds` | Name of the subset GDS file
`sample.include` | Vector of sampleIDs to include in `sub.gds`
`snp.include` | Vector of snpIDs to include in `sub.gds`
`sub.storage` | storage type for the subset file; defaults to original storage type
`compress` | The compression level for variables in a GDS file (see `add.gdsn` for options.
`block.size` | for GDS files stored with scan,snp dimensions, the number of SNPs to read from the parent file at a time. Ignored for snp,scan dimensions.
`verbose` | Logical value specifying whether to show progress information.

### Details

`gdsSubset` can select a subset of snps for all samples by setting `snp.include`, a subset of samples for all snps by setting `sample.include`, or a subset of snps and samples with both arguments. The GDS nodes "snp.id", "snp.position", "snp.chromosome", and "sample.id" are copied, as well as any 2-dimensional nodes. Other nodes are not copied. The attributes of the 2-dimensional nodes are also copied to the subset file. If sub.storage is specified, the subset gds file will have a different storage mode for any 2-dimensional array. In the special case where the 2-dimensional node has an attribute named `"missing.value"` and the sub.storage type is `"bit2"`, the missing.value attribute for the subset node is automatically set to 3. At this point, no checking is done to ensure that the values will be properly stored with a different storage type, but `gdsSubsetCheck` will return an error if the values do not match. If the nodes in the GDS file are stored with scan,snp dimensions, then `block.size` allows you to loop over a block of SNPs at a time. If the nodes are stored with snp,scan dimensions, then the function simply loops over samples, one at a time.

`gdsSubsetCheck` checks that a subset GDS file has the expected SNPs and samples of the parent file. It also checks that attributes were similarly copied, except for the above-mentioned special case of `missing.value` for `sub.storage="bit2"`.

### Author(s)

Adrienne Stilp

### See Also

gdsfmt, `createDataFile`

### Examples

    gdsfile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    gds <- GdsGenotypeReader(gdsfile)
    sample.sel <- getScanID(gds, index=1:10)
    snp.sel <- getSnpID(gds, index=1:100)
    close(gds)

    subfile <- tempfile()
    gdsSubset(gdsfile, subfile, sample.include=sample.sel, snp.include=snp.sel)
    gdsSubsetCheck(gdsfile, subfile, sample.include=sample.sel, snp.include=snp.sel)

    file.remove(subfile)

[Package GWASTools version 1.28.0 Index]