CalculPSSM: Position Specific Scoring Matrices from a set of aligned...
In MEET: MEET: Motif Elements Estimation Toolkit
Description
Usage
Arguments
Value
Author(s)
References
See Also
Examples
Description
Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.
Usage
1
CalculPSSM(matriu, Prob)
Arguments
matriu
Set of DNA aligned sequences
Prob
Probability distribution of the nucleotides in the background model
Value
logodds: logodds matrix calculated as a log2 of the frequency matrix
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
References
Gary D. Stormo. DNA binding sites: representation and discovery. Bioinformatics (2000) 16(1): 16-23 doi:10.1093/bioinformatics/16.1.16
See Also
CalculInformation
Examples
1
2
3
data(TranscriptionFactor)
data(BackgroundOrganism)
CalculPSSM(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
Description
Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.
Usage
1 | CalculPSSM(matriu, Prob)
|
Arguments
matriu |
Set of DNA aligned sequences |
Prob |
Probability distribution of the nucleotides in the background model |
Value
logodds: logodds matrix calculated as a log2 of the frequency matrix
Author(s)
Erola Pairo <epairo@ibecbarcelona.eu>
References
Gary D. Stormo. DNA binding sites: representation and discovery. Bioinformatics (2000) 16(1): 16-23 doi:10.1093/bioinformatics/16.1.16
See Also
CalculInformation
Examples
1 2 3 | data(TranscriptionFactor)
data(BackgroundOrganism)
CalculPSSM(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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