sangerseqAccessors: Sangerseq Accessor Functions

In sangerseqR: Tools for Sanger Sequencing Data in R

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)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

  605-letter "DNAString" instance
seq: GGGGCATAAGARTGTTTTTTAAGGCGCATTCTTTTT...GCTGCTGTATGCTCACAAAACCAATCGAAAGCCTCT
[1] "CCCCGTATTAGGGTGAAAAACCACGCGTAGTCCCGGGATAGTATAATACACCCACCAACCGGCAGAATTACGCATACGCCACTTAAATAGCACACACCGCGCTAAGCGACGGATATCATTCCCGACACGCACACACGGTCGGCGACGGGAACGAGGGAGCCCAACGTGTAGACGAAGCATAAGTGGTCGATTCCGCGGGGGGGGGGACGTAGGTTTTTCTCGGATCCAAGGGGAAAATCTCGGCCTGAATCTCCCCGGAGGTCATCGCTTGAACACCATTAGAAGGGAGGAGAAGTCCATCTAACTAACGTTCCCGGACCAGAGGAACATAGTCAAAAAGAGTCTAGCGGTATACAGAGATACTATGAGCTTGAATAACATGGCGACAACTAGCGCCACGGTTTTATGCGACACAGTCAAGAAAGAAAAACTAAGTTACGGTTCCTCAACATATACTGGAATTTGATCTTATAATGGTTGTAGTTATCACGATGAGTCTGCTATGGGGTAGTCGTATTATCAGGATTCTTATTTATCTCAAACTCAGGTAAACACGGTATAATTGCGATTGGAGCAGCGCAAAGACTTCATCCAAAGGGATTCAA"
[1] "From ab1 file"
[1] "Some string"

sangerseqR documentation built on Nov. 8, 2020, 6:52 p.m.