CalculPSSM: Position Specific Scoring Matrices from a set of aligned...

Description Usage Arguments Value Author(s) References See Also Examples

View source: R/CalculPSSM.R

Description

Calculate a PSSM of a set of DNA aligned sequences, taking into account background probabilities. The output is the logodds matrix.

Usage

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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

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data(TranscriptionFactor)
data(BackgroundOrganism)
CalculPSSM(matriu=TranscriptionFactor, Prob=Prob)

MEET documentation built on May 2, 2019, 5:52 p.m.