selex.kmax {SELEX} | R Documentation |
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.
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
kmax = selex.kmax(sample=r0, threshold=50)