sangerseq-class: Sangerseq Class Objects
In sangerseqR: Tools for Sanger Sequencing Data in R

Description Usage Arguments Slots Accessor methods See Also Examples

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).

sangerseq(obj)

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

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

obj

Can be either an abif or scf object.

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.

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

abif, scf

#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)

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

Formal class 'sangerseq' [package "sangerseqR"] with 7 slots
  ..@ primarySeqID  : chr "From ab1 file"
  ..@ primarySeq    :Formal class 'DNAString' [package "Biostrings"] with 5 slots
  .. .. ..@ shared         :Formal class 'SharedRaw' [package "XVector"] with 2 slots
  .. .. .. .. ..@ xp                    :<externalptr> 
  .. .. .. .. ..@ .link_to_cached_object:<environment: 0x45c80d0> 
  .. .. ..@ offset         : int 0
  .. .. ..@ length         : int 605
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ secondarySeqID: chr "From ab1 file"
  ..@ secondarySeq  :Formal class 'DNAString' [package "Biostrings"] with 5 slots
  .. .. ..@ shared         :Formal class 'SharedRaw' [package "XVector"] with 2 slots
  .. .. .. .. ..@ xp                    :<externalptr> 
  .. .. .. .. ..@ .link_to_cached_object:<environment: 0x45c80d0> 
  .. .. ..@ offset         : int 0
  .. .. ..@ length         : int 605
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ traceMatrix   : int [1:16215, 1:4] 0 0 0 1 2 4 4 2 1 0 ...
  ..@ peakPosMatrix : num [1:605, 1:4] 4 13 21 31 43 58 64 73 83 98 ...
  ..@ peakAmpMatrix : int [1:605, 1:4] 380 694 836 934 1367 1063 2072 1502 1234 539 ...
Formal class 'sangerseq' [package "sangerseqR"] with 7 slots
  ..@ primarySeqID  : chr "From scf file"
  ..@ primarySeq    :Formal class 'DNAString' [package "Biostrings"] with 5 slots
  .. .. ..@ shared         :Formal class 'SharedRaw' [package "XVector"] with 2 slots
  .. .. .. .. ..@ xp                    :<externalptr> 
  .. .. .. .. ..@ .link_to_cached_object:<environment: 0x45c80d0> 
  .. .. ..@ offset         : int 0
  .. .. ..@ length         : int 722
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ secondarySeqID: chr "From scf file"
  ..@ secondarySeq  :Formal class 'DNAString' [package "Biostrings"] with 5 slots
  .. .. ..@ shared         :Formal class 'SharedRaw' [package "XVector"] with 2 slots
  .. .. .. .. ..@ xp                    :<externalptr> 
  .. .. .. .. ..@ .link_to_cached_object:<environment: 0x45c80d0> 
  .. .. ..@ offset         : int 0
  .. .. ..@ length         : int 0
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ traceMatrix   : num [1:16275, 1:4] 187 190 199 220 255 304 354 389 404 402 ...
  ..@ peakPosMatrix : int [1:722, 1:4] 2 18 25 39 45 56 63 68 85 94 ...
  ..@ peakAmpMatrix : num[0 , 0 ]