readsangerseq: Read Scf or ABIF Files

In sangerseqR: Tools for Sanger Sequencing Data in R

Description

This is a convienience function for reading Scf or ABIF files into a sangerseq object, which can be used by the other sangerseq package functions. It is equivalent to calling read.scf or read.abif as appropriate and then calling sangerseq.

Usage

readsangerseq(filename)

Arguments

filename

Location of the file.

Value

sangerseq s4 object

See Also

read.abif, read.scf, abif, scf, sangerseq

Examples

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)

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

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: 0x58dd240> 
  .. .. ..@ 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: 0x58dd240> 
  .. .. ..@ 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: 0x58dd240> 
  .. .. ..@ 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: 0x58dd240> 
  .. .. ..@ 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 ] 

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