sangerseq-class: Sangerseq Class Objects

In jonathonthill/sangerseqR: Tools for Sanger Sequencing Data in R

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)

jonathonthill/sangerseqR documentation built on July 1, 2023, 4:55 p.m.