scf-class: Scf Class Objects

In sangerseqR: Tools for Sanger Sequencing Data in R

Description

S4 object returned by read.scf containing all fields in the SCF file format (see http://staden.sourceforge.net/manual/formats_unix_2.html). Must be converted to sangerseq to be used in other functions from this package.

Slots

header

Header information from the file.

sample_points

Trace data matrix (Order = A, C, G, T).

sequence_probs

Matrix of the relative probabilities for each base at each position (Order = A, C, G, T).

basecall_positions

Vector containing trace matrix indices for each basecall.

basecalls

DNAString object containing the basecalls.

comments

String containing any comments in the file.

private

Raw binary data containing any private data in the file. Generally not used.

See Also

read.scf, abif, sangerseq

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.