selex.kmax: Calculate kmax for a dataset
In SELEX: Functions for analyzing SELEX-seq data

Description Usage Arguments Details Value See Also Examples

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.

1	selex.kmax(sample, threshold=100, seqfilter=NULL)

`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.

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.

selex.kmax returns the kmax value.

selex.counts, selex.mm, selex.sample, selex.seqfilter