R: Get a Data Frame of Base Proportion Data from a...
getBaseProp-methods
R Documentation
Get a Data Frame of Base Proportion Data from a SequenceSummary object
Description
An object that inherits from class SequenceSummary contains
base frequency data by position gathered by readSeqFile. getBaseProp
is an accessor function that reshapes the base frequency data by position
into a data frame and calculates the proportions of each base per position.
This accessor function is useful if you want to map variables to
custom ggplot2 aesthetics. Base frequency be accessed
with getBase.
Usage
getBaseProp(x, drop=TRUE)
Arguments
x
an S4 object that inherits from SequenceSummary from
readSeqFile.
drop
a logical value indicating whether to drop bases that
don't have any counts.
Value
getBaseProp returns a data.frame with columns:
position
the position in the read.
base
the base.
proportion
the proportion of a base found per position in the read.
Methods
signature(x = "SequenceSummary")
getBaseProp is an accessor function that works on any object read
in with readSeqFile; that is, objects that inherit from
SequenceSummary.
## Load a FASTQ file, with sequence hashing.
s.fastq <- readSeqFile(system.file('extdata', 'test.fastq',
package='qrqc'))
# A custom base plot
ggplot(getBaseProp(s.fastq)) + geom_line(aes(x=position, y=proportion,
color=base)) + facet_grid(. ~ base) + scale_color_dna()
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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/getBaseProp-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getBaseProp-methods
> ### Title: Get a Data Frame of Base Proportion Data from a
> ### 'SequenceSummary' object
> ### Aliases: getBaseProp getBaseProp-methods
> ### getBaseProp,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 base plot
> ggplot(getBaseProp(s.fastq)) + geom_line(aes(x=position, y=proportion,
+ color=base)) + facet_grid(. ~ base) + scale_color_dna()
>
>
>
>
>
> dev.off()
null device
1
>