read.scf: Read Scf Files

In sangerseqR: Tools for Sanger Sequencing Data in R

Description

Reads Scf sanger sequencing data files. Scf files are an open source binary sanger sequencing chromatogram data file (see http://staden.sourceforge.net/manual/formats_unix_2.html). The file is read and parsed into an scf class object.

Usage

read.scf(filename)

Arguments

filename

Location of the file.

Value

scf s4 object

See Also

read.abif, readsangerseq, scf

Examples

homoscf <- read.scf(system.file("extdata",
                                "homozygous.scf",
                                package = "sangerseqR"))
str(homoscf)

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, cbind, colMeans, colSums, colnames, 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 'scf' [package "sangerseqR"] with 7 slots
  ..@ header            :Formal class 'scfHeader' [package "sangerseqR"] with 14 slots
  .. .. ..@ scf             : chr ".scf"
  .. .. ..@ samples         : int 16275
  .. .. ..@ samples_offset  : int 128
  .. .. ..@ bases           : int 722
  .. .. ..@ bases_left_clip : int 0
  .. .. ..@ bases_right_clip: int 0
  .. .. ..@ bases_offset    : int 130328
  .. .. ..@ comments_size   : int 1731
  .. .. ..@ comments_offset : int 138992
  .. .. ..@ version         : num 3
  .. .. ..@ sample_size     : int 2
  .. .. ..@ code_set        : int 2
  .. .. ..@ private_size    : int 0
  .. .. ..@ private_offset  : int 140723
  ..@ sample_points     : num [1:16275, 1:4] 187 190 199 220 255 304 354 389 404 402 ...
  ..@ sequence_probs    : int [1:722, 1:4] 0 0 0 0 0 0 0 0 0 0 ...
  ..@ basecall_positions: int [1:722] 2 18 25 39 45 56 63 68 85 94 ...
  ..@ basecalls         : chr "ARGKRAMMYWACTATAGGGCGGAATTGAATTTAGCGGCCGCGAATTCGCCCTTTGGCAAGAGAGCGACAGTCAGTCGGACTTACGAGTTGTTTTTACAGGCGCAATTCTTT"| __truncated__
  ..@ comments          : chr "STRT=6/21/201318:04:27STOP=6/21/201320:02:45SIGN=G=124,A=134,T=204,C=159AEPt=16308AEPt=16308APFN=Seq_AAPXV=APrN"| __truncated__
  ..@ private           : raw [1:2] 00 31

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