This function returns the longest oligonucleotide length k such that all DNA sequences of length k (`K-mers') are found at least a minimum count number of times for the given sample.
Usage
selex.kmax(sample, threshold=100, seqfilter=NULL)
Arguments
sample
A sample handle.
threshold
The minimum count to be used.
seqfilter
A sequence filter object to include/exclude sequences that are read in from the FASTQ file.
Value
selex.kmax returns the kmax value.
Details
The kmax value is used to build the Markov model training and cross-validation datasets. While selex.mm contains a default kmax constructor, running selex.kmax can be useful in building analysis-specific Markov models.
selex.kmax discovers the kmax value by building K-mer count tables; after completion, the K-mer count tables can be viewed using selex.counts. When a new seqfilter object is provided, the kmax value is recomputed. See selex.seqfilter for more details.