selex.infogain: Compute or retrieve information gain between rounds

Description Usage Arguments Details Value References See Also Examples

View source: R/SELEX.R

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

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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

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# 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)]

Bioconductor-mirror/SELEX documentation built on June 1, 2017, 1:14 a.m.