Description Usage Arguments Value See Also Examples
This function plots a histogram of the distribution of sequence complexities
in the form of effective numbers of kmers as determined by seqComplexity
.
By default, kmers of size 2 are used, in which case a perfectly random sequences
will approach an effective kmer number of 16 = 4 (nucleotides) ^ 2 (kmer size).
1 2 3 4 5 6 7 8 9 10 |
fl |
(Required). |
kmerSize |
(Optional). Default 2. The size of the kmers (or "oligonucleotides" or "words") to use. |
window |
(Optional). Default NULL. The width in nucleotides of the moving window. If NULL the whole sequence is used. |
by |
(Optional). Default 5. The step size in nucleotides between each moving window tested. |
n |
(Optional). Default 100,000. The number of records to sample from the fastq file. |
bins |
(Optional). Default 100. The number of bins to use for the histogram. |
aggregate |
(Optional). Default FALSE. If TRUE, compute an aggregate quality profile for all fastq files provided. |
... |
(Optional). Arguments passed on to |
A ggplot2
object.
Will be rendered to default device if printed
,
or can be stored and further modified.
See ggsave
for additional options.
seqComplexity
oligonucleotideFrequency
1 | plotComplexity(system.file("extdata", "sam1F.fastq.gz", package="dada2"))
|
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