FASTQSummary class representing the summaries of a FASTQ file

Description

This class contains the same slots as the SequenceSummary, as well as additional slots for quality information.

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

In addition to the slots inherited from SequenceSummary, FASTQSummary contains:

quality

a string indicating the type of quality (used to convert ASCII characters to quality integers). Either "phred", "solexa", or "illumina".

qual.freqs

a data frame of quality frequencies by position, if the file was a FASTQ file.

mean.qual

a numeric that is the mean quality across all positions, weighted by the number of reads that extended to that position.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

FASTASummary is the counterpart of this class for FASTA data.

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

basePlot is a function that plots the distribution of bases over sequence length for a particular FASTQSummary object. gcPlot combines and plots the GC proportion.

qualPlot is a function that plots the distribution of qualities over sequence length for a particular FASTQSummary object.

seqlenPlot is a function that plots a histogram of sequence lengths for a particular FASTQSummary object.

kmerKLPlot is a function that uses Kullback-Leibler divergence to make a plot that can aid in finding possible contamination (if readSeqFile had kmer=TRUE).

kmerEntropyPlot is a function that plots the Shannon entropy of k-mers per position.

There are acccessor functions getQual, getBase, getBaseProp, getSeqlen, getKmer, getGC for transforming the raw data in the object's slot (direct from the C call) to more usable data frames.

Examples

showClass("FASTQSummary")

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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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/FASTQSummary-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FASTQSummary-class
> ### Title: 'FASTQSummary' class representing the summaries of a FASTQ file
> ### Aliases: FASTQSummary-class makeReport,FASTQSummary-method
> ###   plotQuals,FASTQSummary-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("FASTQSummary")
Class "FASTQSummary" [package "qrqc"]

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

Extends: "SequenceSummary"
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>