CalculInformation: Information content in each position of a set of aligned DNA...
In MEET: MEET: Motif Elements Estimation Toolkit
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
View source: R/CalculInformation.R
Description
Using as an input the set of aligned DNA sequences, information content in each position is calculated, taking into account background probability for each nucleotide. The first row of the returned sequence is the information in each postion, and the others are the loggods matrix.
Usage
1
CalculInformation(matriu, Prob)
Arguments
matriu
Aligned DNA sequences
Prob
Background Probability for the studied individual.
Value
matriu_inf: a matrix with a first row that is the information content in each position and the next ones the logodds matrix using information content.
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
References
T. D. Schneider, G. Stormo, L. Gold, and A. Ehrenfeuch,The information content of binding sites on nucleotide sequences, J. Mol. Biol., vol. 188, Nov. 1986.
See Also
kfold.MATCH, CalculScores.
Examples
1
2
3
4
5
library(MEET)
data(TranscriptionFactor)
data(BackgroundOrganism)
CalculInformation(matriu=TranscriptionFactor, Prob=Prob)
MEET documentation built on May 2, 2019, 5:52 p.m.
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Description Usage Arguments Value Author(s) References See Also Examples
View source: R/CalculInformation.R
Description
Using as an input the set of aligned DNA sequences, information content in each position is calculated, taking into account background probability for each nucleotide. The first row of the returned sequence is the information in each postion, and the others are the loggods matrix.
Usage
1 | CalculInformation(matriu, Prob)
|
Arguments
matriu |
Aligned DNA sequences |
Prob |
Background Probability for the studied individual. |
Value
matriu_inf: a matrix with a first row that is the information content in each position and the next ones the logodds matrix using information content.
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
References
T. D. Schneider, G. Stormo, L. Gold, and A. Ehrenfeuch,The information content of binding sites on nucleotide sequences, J. Mol. Biol., vol. 188, Nov. 1986.
See Also
kfold.MATCH, CalculScores.
Examples
1 2 3 4 5 | library(MEET)
data(TranscriptionFactor)
data(BackgroundOrganism)
CalculInformation(matriu=TranscriptionFactor, Prob=Prob)
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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