An object that inherits from class
k-mer frequency data by position gathered by
getKmer is an accessor function that is
useful for custom
an S4 object that inherits from class
getKmer returns a
data.frame with columns:
the k-mer sequence.
the position in the read.
the frequency of the k-mer at this position.
getKmer is an accessor function that only works if there is
k-mer data, thus it only works if
readSeqFile was called
hash.prop is greater than 0).
Vince Buffalo <[email protected]>
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## Load a FASTQ file, with sequence and k-mer hashing on by default. s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc')) ## plot counts of a subset of k-mers by position s.kmers <- getKmer(s.fastq) top.kmers <- s.kmers$kmer[order(s.kmers$count, decreasing=TRUE)[1:40]] p <- ggplot(subset(s.kmers, kmer %in% top.kmers)) + geom_bar(aes(x=position, y=count, fill=kmer), stat="identity") p
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