FASTASummary class representing the summaries of a FASTA file

Description

This class contains the same slots as the SequenceSummary, but it is used to indicate the data originated from a FASTA file.

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

FASTASummary has the slots inherited from SequenceSummary.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

FASTQSummary is the counterpart of this class for FASTQ data.

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

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

seqlenPlot is a function that plots a histogram of sequence lengths for a particular FASTASummary 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("FASTASummary")

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/FASTASummary-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: FASTASummary-class
> ### Title: 'FASTASummary' class representing the summaries of a FASTA file
> ### Aliases: FASTASummary-class makeReport,FASTASummary-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("FASTASummary")
Class "FASTASummary" [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

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