seqMerge {SeqArray} | R Documentation

## Merge Multiple SeqArray GDS Files

### Description

Merges multiple SeqArray GDS files.

### Usage

    seqMerge(gds.fn, out.fn, storage.option="LZMA_RA", info.var=NULL, fmt.var=NULL,
        samp.var=NULL, optimize=TRUE, digest=TRUE, geno.pad=TRUE, verbose=TRUE)

### Arguments

`gds.fn` | the file names of multiple GDS files
`out.fn` | the output file name
`storage.option` | specify the storage and compression option, "ZIP_RA" (`seqStorageOption("ZIP_RA")`); or "LZMA_RA" to use LZMA compression algorithm with higher compression ratio (by default)
`info.var` | characters, the variable name(s) in the INFO field; `NULL` for all variables, or `character()` excludes all INFO variables
`fmt.var` | characters, the variable name(s) in the FORMAT field; `NULL` for all variables, or `character()` excludes all FORMAT variables
`samp.var` | characters, the variable name(s) in 'sample.annotation'; or `NULL` for all variables
`optimize` | if `TRUE`, optimize the access efficiency by calling `cleanup.gds`
`digest` | a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); add md5 hash codes to the GDS file if TRUE or a digest algorithm is specified
`geno.pad` | TRUE, pad a 2-bit genotype array in bytes to avoid recompressing genotypes if possible
`verbose` | if `TRUE`, show information

### Details

The function merges multiple SeqArray GDS files. Users can specify the compression method and level for the new GDS file. If `gds.fn` contains one file, users can change the storage type to create a new file.

WARNING: the functionality of `seqMerge()` is limited.

### Value

Return the file name of GDS format with an absolute path.

### Author(s)

Xiuwen Zheng

### See Also

`seqVCF2GDS`, `seqExport`

### Examples

    # the VCF file
    vcf.fn <- seqExampleFileName("vcf")

    # the number of variants
    total.count <- seqVCF_Header(vcf.fn, getnum=TRUE)$num.variant

    split.cnt <- 5
    start <- integer(split.cnt)
    count <- integer(split.cnt)

    s <- (total.count+1) / split.cnt
    st <- 1L
    for (i in 1:split.cnt)
    {
        z <- round(s * i)
        start[i] <- st
        count[i] <- z - st
        st <- z
    }

    fn <- paste0("tmp", 1:split.cnt, ".gds")

    # convert to 5 gds files
    for (i in 1:split.cnt)
    {
        seqVCF2GDS(vcf.fn, fn[i], storage.option="ZIP_RA",
            start=start[i], count=count[i])
    }

    # merge
    seqMerge(fn, "tmp.gds", storage.option="ZIP_RA")
    seqSummary("tmp.gds")

    ####

    vcf.fn <- seqExampleFileName("gds")
    file.copy(vcf.fn, "test.gds", overwrite=TRUE)

    # modify 'sample.id'
    f <- openfn.gds("test.gds", FALSE)
    sid <- read.gdsn(index.gdsn(f, "sample.id"))
    add.gdsn(f, "sample.id", paste("S", 1:length(sid)), replace=TRUE)
    closefn.gds(f)

    # merging
    seqMerge(c(vcf.fn, "test.gds"), "output.gds", storage.option="ZIP_RA")

    # delete the temporary files
    unlink(c("tmp.gds", "test.gds", "output.gds"), force=TRUE)
    unlink(fn, force=TRUE)

[Package SeqArray version 1.26.2 Index]