selex.counts {SELEX} | R Documentation

## Construct or retrieve a K-mer count table

### Description

A function used to count and return the number of instances K-mers of length `k` appear within the `sample`'s variable regions. If an `offset` value is provided, K-mer counting takes place at a fixed position within the variable region of the read. If a Markov model is supplied, the expected count and the probability of observing the K-mer are also returned.

### Usage

    selex.counts(sample, k, minCount=100, top=-1, numSort=TRUE, offset=NULL,
      markovModel=NULL, forceCalculation=FALSE, seqfilter=NULL, outputPath = "")

### Arguments

`sample` | A sample handle to the dataset on which K-mer counting should be perfomed.
`k` | K-mer length(s) to be counted.
`minCount` | The minimum number of counts for a K-mer to be output.
`top` | Give the first N K-mers (by count).
`numSort` | Sort K-mers in descending order by count. If `FALSE`, K-mers are sorted in ascending order.
`offset` | Location of window for which K-mers should be counted for. If not provided, K-mers are counted across all windows.
`markovModel` | Markov model handle to use to predict previous round probabilities and expected counts.
`forceCalculation` | Forces K-mer counting to be performed again, even if a previous result exists.
`seqfilter` | A sequence filter object to include/exclude sequences that are read in from the FASTQ file.
`outputPath` | Prints the computed K-mer table to a plain text file. This is useful when the number of unique K-mers in the dataset exceeds R's memory limit.

### Details

The `offset` feature counts K-mers of length `k` `offset` bp away from the 5' end in the variable region. For example, if we have 16-mer variable regions and wish to count K-mers of length 12 at an offset of 3 bp, we are looking at the K-mers found only at the position indicated by the bolded nucleotides in the variable region:
5' NNNNNNNNNNNNNNNN 3'
Minimum count refers to the lowest count observed for a kmer of length k for a given sample. Total count is the sum of counts over all kmers of length k for a given sample. These statistics can be viewed for all K-mer lengths and samples counting was performed on using `selex.countSummary`. When a new `seqfilter` object is provided, K-mer counting is redone. See `selex.seqfilter` for more details.
See ‘References’ for more details regarding the K-mer counting process.

### Value

`selex.counts` returns a data frame containing the K-mer sequence and observed counts for a given sample if a Markov model has not been supplied.
If a Markov model is supplied, a data frame containing K-mer sequence, observed counts, predicted previous round probability, and predicted previous round expected counts is returned.
If the number of unique K-mers exceeds R's memory limit, `selex.counts` will cause R to crash when returning a data frame containing the K-mers. The `outputPath` option can be used to avoid such a situation, as the Java code will directly write the table to a plain text file at the specified location instead.

### References

Slattery, M., Riley, T.R., Liu, P., Abe, N., Gomez-Alcala, P., Dror, I., Zhou, T., Rohs, R., Honig, B., Bussemaker, H.J.,and Mann, R.S. (2011) Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins. Cell 147:1270–1282.

Riley, T.R., Slattery, M., Abe, N., Rastogi, C., Liu, D., Mann, R.S., and Bussemaker, H.J. (2014) SELEX-seq: a method for characterizing the complete repertoire of binding site preferences for transcription factor complexes. Methods Mol. Biol. 1196:255–278.

### See Also

`selex.affinities`, `selex.countSummary`, `selex.infogain`, `selex.kmax`, `selex.mm`, `selex.run`

### Examples

    # Kmer counting for a specific length on a given dataset
    t1 = selex.counts(sample=r2, k=8, minCount=1)

    # Kmer counting with an offset
    t2 = selex.counts(sample=r2, k=2, offset=14, markovModel=NULL)

    # Kmer counting with a Markov model (produces expected counts)
    t3 = selex.counts(sample=r2, k=4, markovModel=mm)

    # Display all available kmer statistics
    selex.countSummary()

[Package SELEX version 1.12.0 Index]