Description Usage Arguments Details Value References See Also Examples

A function used to compute and store the information gain for various K-mer lengths on `sample`

using `markovModel`

to predict prior probabilities.

1 2 | ```
selex.infogain(sample, k=NULL, markovModel, seqfilter=NULL,
checkBarcode=TRUE)
``` |

`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 |

`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. |

`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.

`selex.infogain`

returns the highest information gain value.

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.

`selex.infogainSummary`

, `selex.mm`

, `selex.run`

1 2 3 4 5 6 7 8 9 10 11 | ```
# 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.

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