SELEX (version 1.4.0)

selex.affinities: 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.

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.

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.

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)