SequenceSummary class representing the summaries of a sequence file

Description

A sequence file read in with readSeqFile is summarized by a C call. This is a base class with slots common to both FASTQSummary and FASTASummary. This is not usually instantiated directly.

Note that many accessor functions transform data in the slots into data frames. The data in the slots is mostly untransformed and less easy to work with directly, so using the accessor functions is recommended.

Slots

filename

the filename processed by readSeqFile.

base.freqs

a data frame of base frequencies by position. Each column is a nucleotide (there is a column for position too), and each row contains the count frequencies of bases for that position.

seq.lengths

a numeric vector of the number of sequences of a particular length (the length is the position in the vector).

hash

a numeric vector of the count frequencies of sequences (the sequences are in the name attribute).

hash.prop

a numeric value indicating the proportion of sequences that were sampled for hashing.

kmer

a data frame of k-mer frequency by position.

k

an integer indicating the length of k-mers hashed.

hashed

a logical indicating whether the sequences were hashed in readSeqFile.

kmers.hashed

a logical indicating whether the k-mers were hashed in readSeqFile.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

FASTQSummary and FASTASummary are the classes that inherit from SequenceSummary.

readSeqFile is the function that takes a FASTQ or FASTA file and returns a FASTQSummary object or FASTASummary object.

Examples

showClass("SequenceSummary")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(qrqc)
Loading required package: reshape
Loading required package: ggplot2
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, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand, rename

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: biovizBase
Loading required package: brew
Loading required package: xtable
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: testthat

Attaching package: 'testthat'

The following object is masked from 'package:S4Vectors':

    compare

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/qrqc/SequenceSummary-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: SequenceSummary-class
> ### Title: 'SequenceSummary' class representing the summaries of a sequence
> ###   file
> ### Aliases: SequenceSummary-class plotBases,SequenceSummary-method
> ###   plotGC,SequenceSummary-method plotSeqLengths,SequenceSummary-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("SequenceSummary")
Virtual Class "SequenceSummary" [package "qrqc"]

Slots:
                                                                       
Name:      filename   base.freqs  seq.lengths         hash    hash.prop
Class:    character   data.frame      integer      numeric      numeric
                                                          
Name:          kmer            k       hashed kmers.hashed
Class:   data.frame      integer      logical      logical

Known Subclasses: "FASTASummary", "FASTQSummary"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>