selex.affinities {SELEX} | R Documentation

## Construct a K-mer affinity table

### Description

A function used to calculate and return the affinities and affinity standard errors of K-mers of length `k` for a given dataset in addition to all the output provided by `selex.counts`. A Markov model is necessary for evaluation.

### Usage

    selex.affinities(sample, k, minCount=100, top=-1, numSort=TRUE, offset=NULL,
    	markovModel=NULL, seqfilter=NULL)

### 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 alphabetically.
`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.
`seqfilter` | A sequence filter object to include/exclude sequences that are read in from the FASTQ file.

### Details

When a new `seqfilter` object is provided, K-mer counting and affinity table construction is redone. See `selex.seqfilter` for more details.

See ‘References’ for more details regarding K-mer counting and affinity calculation.

### Value

`selex.affinities` returns a data frame containing the K-mer sequence, observed counts, predicted prior observation probability, predicted prior observed counts, affinities, and standard errors.

### 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.counts`, `selex.infogain`, `selex.kmax`, `selex.mm`

### Examples

    r2Aff = selex.affinities(sample=r2, k=10, markovModel=mm)

[Package SELEX version 1.16.0 Index]