seqSummary {SeqArray} | R Documentation

## Summarize a SeqArray GDS File

### Description

Gets the summary of SeqArray GDS file.

### Usage

    seqSummary(gdsfile, varname=NULL, check=c("default", "none", "full"),
        verbose=TRUE)

### Arguments

`gdsfile` | a `SeqVarGDSClass` object, or a file name
`varname` | if `NULL`, check the whole GDS file; or a character specifying variable name, and return a description of that variable. See details
`check` | should be one of "default", "none", "full"
`verbose` | if `TRUE`, display information

### Details

If `check="default"`, the function performs regular checking, like variable dimensions. If `check="full"`, it performs more checking, e.g., unique sample id, unique variant id, whether genotypic data are in a valid range or not.

### Value

If `varname=NULL`, the function returns a list:

`filename` | the file name
`version` | the version of SeqArray format
`reference` | genome reference, a character vector (0-length for undefined)
`ploidy` | the number of sets of chromosomes
`num.sample` | the total number of samples
`num.variant` | the total number of variants
`allele` | allele information, see `seqSummary(gdsfile, "allele")`
`annot_qual` | the total number of "annotation/qual" if `check="none"`, or a summary object including min, max, median, mean
`filter` | filter information, see `seqSummary(gdsfile, "annotation/filter")`
`info` | a `data.frame` of INFO field: ID, Number, Type, Description, Source and Version
`format` | a `data.frame` of FORMAT field: ID, Number, Type and Description
`sample.annot` | a `data.frame` of sample annotation with ID, Type and Description

— `seqSummary(gdsfile, "genotype", check="none", verbose=FALSE)` returns a list with components:

`dim` | an integer vector: ploidy, # of samples, # of variants
`seldim` | an integer vector: ploidy, # of selected samples, # of selected variants

— `seqSummary(gdsfile, "allele")` returns a data.frame with ID and descriptions (`check="none"`), or a list with components:

`value` | a data.frame with ID and Description
`table` | cross tabulation for the number of alleles per site

— `seqSummary(gdsfile, "$alt")` returns a data.frame with ID and Description for describing the alternative alleles.

— `seqSummary(gdsfile, "annotation/filter")` or `seqSummary(gdsfile, "$filter")` returns a data.frame with ID and description (`check="none"`), or a list with components:

`value` | a data.frame with ID and Description
`table` | cross tabulation for the variable 'filter'

— `seqSummary(gdsfile, "annotation/info")` or `seqSummary(gdsfile, "$info")` returns a `data.frame` describing the variables in the folder "annotation/info" with ID, Number, Type, Description, Source and Version.

— `seqSummary(gdsfile, "annotation/format")` returns a `data.frame` describing the variables in the folder "annotation/format" with ID, Number, Type and Description.

— `seqSummary(gdsfile, "sample.annotation")` returns a `data.frame` describing sample annotation with ID, Type and Description.

— `seqSummary(gdsfile, "$reference")` returns the genome reference if it is defined (a 0-length character vector if undefined).

— `seqSummary(gdsfile, "$contig")` returns the contig information, a `data.frame` including ID.

— `seqSummary(gdsfile, "$format")` returns a `data.frame` describing VCF FORMAT header with ID, Number, Type and Description. The first row is used for genotypes.

— `seqSummary(gdsfile, "$digest")` returns a `data.frame` with the full names of GDS variables, digest codes and validation (FALSE/TRUE).

### Author(s)

Xiuwen Zheng

### See Also

`seqGetData`, `seqApply`

### Examples

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

    seqSummary(gds.fn)

    ans <- seqSummary(gds.fn, check="full")
    ans

    seqSummary(gds.fn, "genotype")
    seqSummary(gds.fn, "allele")
    seqSummary(gds.fn, "annotation/filter")
    seqSummary(gds.fn, "annotation/info")
    seqSummary(gds.fn, "annotation/format")
    seqSummary(gds.fn, "sample.annotation")

    seqSummary(gds.fn, "$reference")
    seqSummary(gds.fn, "$contig")
    seqSummary(gds.fn, "$filter")
    seqSummary(gds.fn, "$alt")
    seqSummary(gds.fn, "$info")
    seqSummary(gds.fn, "$format")
    seqSummary(gds.fn, "$digest")

    # open a GDS file
    f <- seqOpen(gds.fn)

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

    seqSummary(f, "genotype")

    # close a GDS file
    seqClose(f)

[Package SeqArray version 1.26.2 Index]