plotNucCount {seqTools} | R Documentation |
The function creates plots from nucleotide counts from Fastqq objects.
plotNucCount(object, nucs=16, maxx,...)
object |
|
nucs |
|
maxx |
|
... |
(currently unused). |
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).
None.
Wolfgang Kaisers
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
Fastqq-class
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")) # plotNucCount(fq) plotNucCount(fq, 1) plotNucCount(fq, 1:2) #