selex.infogain {SELEX} | R Documentation

## Compute or retrieve information gain between rounds

### Description

A function used to compute and store the information gain for various K-mer lengths on `sample` using `markovModel` to predict prior probabilities.

### Usage

    selex.infogain(sample, k=NULL, markovModel, seqfilter=NULL,
      checkBarcode=TRUE)

### Arguments

`sample` | A sample handle to the dataset on which to perform the analysis.
`k` | The range of K-mer lengths for which the information gain should be calculated. If `NA`, the range is automatically set to start from the optimal Markov model order + 1 to the length of the variable region.
`markovModel` | A Markov model handle.
`seqfilter` | A sequence filter object to include/exclude sequences that are read in from the FASTQ file.
`checkBarcode` | Checks to see if the sample barcodes used to construct the Markov model match those in the current sample, and prevents computation if they do not match.

### Details

`selex.infogainSummary` is required to view the computed information gain values. When a new `seqfilter` object is provided, the information gain analysis is redone. See `selex.seqfilter` for more details.
See ‘References’ for more on the computation of information gain values.

### Value

`selex.infogain` returns the highest information gain value.

### 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.infogainSummary`, `selex.mm`, `selex.run`

### Examples

    # Calculate information gain for a fixed range
    ig1 =  selex.infogain(sample=r2, k=c(8:10), markovModel=mm)

    # View the results
    selex.infogainSummary()[,c(1,2,3,4,5)]

    # Now calculate for the default range
    ig2 = selex.infogain(sample=r2, markovModel=mm)

    # View the results again
    selex.infogainSummary()[,c(1,2,3,4,5)]

[Package SELEX version 1.16.0 Index]