calcKL-methods {qrqc} | R Documentation |
calcKL
takes in an object that inherits from
SequenceSummary
that has a kmers slot, and returns the terms of
the K-L divergence sum (which correspond to items in the sample space,
in this case, k-mers).
calcKL(x)
x |
an S4 object a class that inherits from |
calcKL
returns a data.frame
with columns:
kmer |
the k-mer sequence. |
position |
the position in the read. |
kl |
the K-L term for this k-mer in the K-L sum, calculated as p(i)*log2(p(i)/q(i)). |
p |
the probability for this k-mer, at this position. |
q |
the probability for this k-mer across all positions. |
The K-L divergence calculation in calcKL
uses base 2 in the
log; the units are in bits.
Vince Buffalo <vsbuffalo@ucdavis.edu>
## Load a somewhat contaminated FASTQ file s.fastq <- readSeqFile(system.file('extdata', 'test.fastq', package='qrqc'), hash.prop=1) ## As with getQual, this function is provided so custom graphics can ## be made easily. For example K-L divergence by position: kld <- with(calcKL(s.fastq), aggregate(kl, list(position), sum)) colnames(kld) <- c("position", "KL") p <- ggplot(kld) + geom_line(aes(x=position, y=KL), color="blue") p + scale_y_continuous("K-L divergence")