Get a Data Frame of k-mer Frequency by Position from a SequenceSummary Object

Description

An object that inherits from class SequenceSummary contains k-mer frequency data by position gathered by readSeqFile when kmer=TRUE. getKmer is an accessor function that is useful for custom ggplot2 aesthetics.

Usage

getKmer(x)

Arguments

Value

getKmer returns a data.frame with columns:

Methods

signature(x="SequenceSummary")

getKmer is an accessor function that only works if there is k-mer data, thus it only works if readSeqFile was called with kmer=TRUE (and hash.prop is greater than 0).

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

getGC, getSeqlen, getBase, getBaseProp, getQual, getMCQual, kmerKLPlot, kmerEntropyPlot

Examples

  ## Load a FASTQ file, with sequence and k-mer hashing on by default.
  s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))

  ## plot counts of a subset of k-mers by position
  s.kmers <- getKmer(s.fastq)
  top.kmers <- s.kmers$kmer[order(s.kmers$count, decreasing=TRUE)[1:40]]
  p <- ggplot(subset(s.kmers, kmer %in% top.kmers)) + geom_bar(aes(x=position, y=count,
    fill=kmer), stat="identity")
  p

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/getKmer-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getKmer-methods
> ### Title: Get a Data Frame of k-mer Frequency by Position from a
> ###   'SequenceSummary' Object
> ### Aliases: getKmer getKmer-methods getKmer,SequenceSummary-method
> ### Keywords: methods accessor
> 
> ### ** Examples
> 
>   ## Load a FASTQ file, with sequence and k-mer hashing on by default.
>   s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'))
> 
>   ## plot counts of a subset of k-mers by position
>   s.kmers <- getKmer(s.fastq)
>   top.kmers <- s.kmers$kmer[order(s.kmers$count, decreasing=TRUE)[1:40]]
>   p <- ggplot(subset(s.kmers, kmer %in% top.kmers)) + geom_bar(aes(x=position, y=count,
+     fill=kmer), stat="identity")
>   p
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>