Get a Data Frame of GC Content from a SequenceSummary object

Description

An object that inherits from class SequenceSummary contains base frequency data by position gathered by readSeqFile. getGC is an accessor function that reshapes the base frequency data into a data frame and returns the GC content by position.

This accessor function is useful if you want to map variables to custom ggplot2 aesthetics. Frequencies or proportions of all bases (not just GC) can be accessed with getBase and getBaseProp respectively.

Usage

  getGC(x)

Arguments

Value

getGC returns a data.frame with columns:

Methods

signature(x = "SequenceSummary")

getGC is an accessor function that works on any object read in with readSeqFile; that is, objects that inherit from SequenceSummary.

Author(s)

Vince Buffalo <vsbuffalo@ucdavis.edu>

See Also

getSeqlen, getBase, getBaseProp, getQual, getMCQual, getKmer, gcPlot

Examples

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

  # A custom GC plot
  d <- merge(getQual(s.fastq), getGC(s.fastq), by.x="position", by.y="position")
  p <- ggplot(d) + geom_linerange(aes(x=position, ymin=lower,
    ymax=upper, color=gc)) + scale_color_gradient(low="red",
    high="blue") + scale_y_continuous("GC content")
  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
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> 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/getGC-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getGC-methods
> ### Title: Get a Data Frame of GC Content from a 'SequenceSummary' object
> ### Aliases: getGC getGC-methods getGC,SequenceSummary-method
> ### Keywords: methods accessor
> 
> ### ** Examples
> 
>   ## Load a FASTQ file, with sequence hashing.
>   s.fastq <- readSeqFile(system.file('extdata', 'test.fastq',
+     package='qrqc'))
> 
>   # A custom GC plot
>   d <- merge(getQual(s.fastq), getGC(s.fastq), by.x="position", by.y="position")
>   p <- ggplot(d) + geom_linerange(aes(x=position, ymin=lower,
+     ymax=upper, color=gc)) + scale_color_gradient(low="red",
+     high="blue") + scale_y_continuous("GC content")
>   p
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>