selex.kmax {SELEX} | R Documentation

## Calculate kmax for a dataset

### Description

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.

### 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.

### Value

`selex.kmax` returns the kmax value.

### See Also

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

### Examples

    kmax = selex.kmax(sample=r0, threshold=50)

[Package SELEX version 1.19.5 Index]