sangerseq-class {sangerseqR} | R Documentation

## Sangerseq Class Objects

### Description

Sangerseq Class Objects contain data necessary for using sangerseq package functions (e.g. `chromatogram`, `makeBaseCalls`). The exact content will depend on the source of the data (for example, scf files do not have secondary Basecalls).

### Usage

    sangerseq(obj)

    ## S4 method for signature 'abif'
    sangerseq(obj)

    ## S4 method for signature 'scf'
    sangerseq(obj)

### Arguments

`obj` | Can be either an `abif` or `scf` object.

### Slots

`primarySeqID`

  Source of the primary basecalls. Functions that modify these calls, such as `makeBaseCalls` and `setAllelePhase` will also change this value.

`secondarySeqID`

  Source of the secondary basecalls. See above.

`primarySeq`

  The primary Basecalls formatted as a `DNAString` object.

`secondarySeq`

  The secondary Basecalls formatted as a `DNAString` object.

`traceMatrix`

  A numerical matrix containing 4 columns corresponding to the normalized signal values for the chromatogram traces. Column order = A,C,G,T.

`peakPosMatrix`

  A numerical matrix containing the position of the maximum peak values for each base within each Basecall window. If no peak was detected for a given base in a given window, then "NA". Column order = A,C,G,T.

`peakAmpMatrix`

  A numerical matrix containing the maximum peak amplitudes for each base within each Basecall window. If no peak was detected for a given base in a given window, then 0. Column order = A,C,G,T.

### Accessor methods

`primarySeqID`, `primarySeq`, `secondarySeqID`, `secondarySeq`, `traceMatrix`, `peakPosMatrix`, `peakAmpMatrix`

### See Also

`abif`, `scf`

### Examples

    #sample sangerseq object created from abif file
    hetsangerseq <- readsangerseq(system.file("extdata",
                                              "heterozygous.ab1",
                                              package = "sangerseqR"))
    str(hetsangerseq)
    #same for scf files
    homosangerseq <- readsangerseq(system.file("extdata",
                                               "homozygous.scf",
                                               package = "sangerseqR"))
    str(homosangerseq)

[Package sangerseqR version 1.18.0 Index]