SeqSQC-class {SeqSQC} | R Documentation

## A data format to store genotype phenotype and sample QC results from SeqSQC.

### Description

A SeqSQC object is a list of two objects. The first object `gdsfile` is the filepath of the GDS (discussed in section below) file which stores the genotype information from the original VCF file. The second object `QCresult` is a list of sample information and QC results, which include the dimension (# of samples and variants), sample annotation, and QC results for sample missing rate, sex check, inbreeding outlier check, IBD check, and population outlier check.

### Usage

    SeqSQC(gdsfile, QCresult = List())

    gdsfile(x)

    gdsfile(x) <- value

    QCresult(x)

    QCresult(x) <- value

    ## S4 method for signature 'SeqSQC'
    gdsfile(x)

    ## S4 replacement method for signature 'SeqSQC'
    gdsfile(x) <- value

    ## S4 method for signature 'SeqSQC'
    QCresult(x)

    ## S4 replacement method for signature 'SeqSQC'
    QCresult(x) <- value

### Arguments

`gdsfile` | A character string for the filepath of the GDS file.
`QCresult` | A list with sample information and sample QC results.
`x` | an SeqSQCClass object.
`value` | the new value for the SeqSQC object slots.

### Value

The filepath to the gds file.

### Slots

`gdsfile`

  A character string for the filepath of the GDS file.

`QCresult`

  A list with sample information and sample QC results.

### Examples

    load(system.file("extdata", "example.seqfile.Rdata", package="SeqSQC"))
    gdsfile(seqfile)
    QCresult(seqfile)

[Package SeqSQC version 1.6.0 Index]