sangerseqAccessors: Sangerseq Accessor Functions

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

Sangerseq Accessor Functions

Description

Accessor Functions allow the user to retrieve results from and assign values to sangerseq-class objects.

Usage

primarySeqID(obj)

primarySeqID(obj) <- value

primarySeq(obj, string = FALSE)

primarySeq(obj) <- value

secondarySeqID(obj)

secondarySeqID(obj) <- value

secondarySeq(obj, string = FALSE)

secondarySeq(obj) <- value

traceMatrix(obj)

traceMatrix(obj) <- value

peakPosMatrix(obj)

peakPosMatrix(obj) <- value

peakAmpMatrix(obj)

peakAmpMatrix(obj) <- value

## S4 method for signature 'sangerseq'
primarySeq(obj, string = FALSE)

## S4 method for signature 'sangerseq'
secondarySeq(obj, string = FALSE)

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

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

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

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

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

## S4 replacement method for signature 'sangerseq'
primarySeq(obj) <- value

## S4 replacement method for signature 'sangerseq'
secondarySeq(obj) <- value

## S4 replacement method for signature 'sangerseq'
traceMatrix(obj) <- value

## S4 replacement method for signature 'sangerseq'
peakPosMatrix(obj) <- value

## S4 replacement method for signature 'sangerseq'
peakAmpMatrix(obj) <- value

## S4 replacement method for signature 'sangerseq'
primarySeqID(obj) <- value

## S4 replacement method for signature 'sangerseq'
secondarySeqID(obj) <- value

Arguments

obj	sangerseq object to be manipulated
value	The value to set the slot to.
string	TRUE/FALSE. FALSE (default) returns a DNAString class object. TRUE returns the DNA sequence as a character string.

See Also

sangerseq-class

Examples

hetsangerseq <- readsangerseq(system.file("extdata", 
                                          "heterozygous.ab1", 
                                          package = "sangerseqR"))
primarySeq(hetsangerseq)
secondarySeq(hetsangerseq, string=TRUE)
primarySeqID(hetsangerseq)
primarySeqID(hetsangerseq) <- "Some string"
primarySeqID(hetsangerseq)

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