R: plotNucCount: Plots nucleotide counts from Fastqq objects.
plotNucCount
R Documentation
plotNucCount: Plots nucleotide counts from Fastqq objects.
Description
The function creates plots from nucleotide counts
from Fastqq objects.
Usage
plotNucCount(object, nucs=16, maxx,...)
Arguments
object
Fastqq: Object which contains collected values from
nFiles FASTQ files.
nucs
integer(optional): Index of nucleotides for which data
is plotted. When value is missing, k-mer counts for all contained data
is plotted.
maxx
integer(optional): When given, nucleotide counts are
plotted for the first maxx nucleotide positions. This option is used
for displaying detailed plots from the first read nucleotide positions
(which are sometimes not equally distributed).
...
(currently unused).
Details
Values for i must be in {1,...,nFiles}. The nucs index encodes for
IUPAC characters as shown in the following table.
1
A
|
6
R
|
11
M
|
16
N
2
C
|
7
Y
|
12
B
|
17
.
3
G
|
8
S
|
13
D
|
18
-
4
T
|
9
W
|
14
H
|
19
=
5
U
|
10
K
|
15
V
|
20
''
When count values for 'A' are to be plotted, 'nucs' must be =1. When count
values for 'GC' are to be plotted, 'nucs' must be c(2,3).
Value
None.
Author(s)
Wolfgang Kaisers
References
Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM
The sanger FASTQ file format for sequences with quality scores and
the Solexa/Illumina FASTQ variants.
Nucleic Acids Research 2010 Vol.38 No.6 1767-1771
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(seqTools)
Loading required package: zlibbioc
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/seqTools/plotNucCount.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotNucCount
> ### Title: plotNucCount: Plots nucleotide counts from Fastqq objects.
> ### Aliases: plotNucCount plotNucCount-methods plotNucCount,Fastqq-method
> ### Keywords: plotNucCount kmer
>
> ### ** Examples
>
> basedir <- system.file("extdata", package="seqTools")
> setwd(basedir)
> #
> fq <- fastqq(c("g4_l101_n100.fq.gz", "g5_l101_n100.fq.gz"), k=4,
+ probeLabel=c("g4", "g5"))
[fastqq] File ( 1/2) 'g4_l101_n100.fq.gz' done.
[fastqq] File ( 2/2) 'g5_l101_n100.fq.gz' done.
> #
> plotNucCount(fq)
> plotNucCount(fq, 1)
> plotNucCount(fq, 1:2)
> #
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.
